Papers & Results
Peer-reviewed publications that used directly or are closely connected to Folding@home simulations, chronological by year. Many entries link to PubMed or the original journal; recent entries link to the F@H news post that announced the work.
If a link is paywalled, Google Scholar usually finds an open-access version. For broader project background, see the Folding@home article on Wikipedia.
2026
TitleGroup
- Large-Scale Collaborative Assessment of Binding Free Energy Calculations for Drug Discovery Using OpenFEChodera
- Solvent Environment Influences Molecular Conformation and Electron Transport in PeptidesShukla
- Molecular Dynamics Workflows to Compute Large-Scale Sets of Absolute Binding Free Energies Aiding Drug Candidate and Binding Pose SelectionLindahl
- Developing and Benchmarking Sage 2.3.0 with the AshGC Neural Network Charge ModelChodera
- Deep mining of the human antibody repertoire identifies frequent and genetically diverse CDRH3 topologies targetable by vaccinationBowman
- How Well Can AI and Physics-Based Simulations Predict the Probability a Cryptic Pocket Is Open?Bowman
- Dynamic mechanism for subtype selectivity of endocannabinoidsShukla
- De novo Folding Mechanisms of Lasso PeptidesShukla
- More protein-ligand data are needed for AlphaFold-like models to enable drug discoveryChodera
- Introduction to Markov State Modeling of Conformational DynamicsBowman
- A Computational Community Blind Challenge on Pan-Coronavirus Drug Discovery DataChodera
- Multiple modes of cholesterol translocation in the human Smoothened receptorShukla
- Automatic forward model parameterization with Bayesian inference of conformational populationsVoelz
- How Minor Sequence Changes Enable Mechanistic Diversity in MFS Transporters? An Atomic-Level Rationale for Symport Emergence in NarUShukla
- Blind Challenges Let Us See the Path Forward for Predictive ModelsChodera
- Decrypting cryptic pockets with physics-based simulations and artificial intelligenceBowman
- Structural dynamics of adenine nucleotide potentiation of the human type 2 IP(3) receptorChodera
- Sequence constraints predispose Class D GPCRs to follow an atypical activation mechanismShukla
- The Yeh pilus adhesin is equipped with an α-helical flap motif, which contributes to pectin adherenceBowman
- All roads lead to Rome: Emergence of Mechanistic Divergence Shapes Activation of Class B1 G-Protein Coupled ReceptorsShukla
2025
TitleGroup
- Calcium stabilizes the flexible N-terminal domain of the bacterial ion channel DeCLICLindahl
- How minor sequence changes enable mechanistic diversity in MFS transporters? An atomic-level rationale for symport emergence in NarUShukla
- Multi-scale simulations of MUT-16 scaffold protein phase separation and client recognitionHanson/Cossio
- Characterization of binding kinetics and intracellular signaling of new psychoactive substances targeting cannabinoid receptor using transition-based reweighting methodShukla
- Modeling cryo-EM structures in alternative states with AlphaFold2-based models and density-guided simulationsLindahl
- The G Protein Inhibitor YM-254890 is an Allosteric GlueBowman
- Structural Basis for Negative Regulation of ABA Signaling by ROP11 GTPaseShukla
- How many crystal structures do you need to trust your docking results?Chodera
- Opening and closing of a cryptic pocket in VP35 toggles it between two different RNA-binding modesBowman
- Massively Parallel Free Energy Calculations for In Silico Affinity Maturation of Designed MiniproteinsVoelz
- Microbiota-derived corisin accelerates kidney fibrosis by promoting cellular agingShukla
- ESMDynamic: Fast and Accurate Prediction of Protein Dynamic Contact Maps from Single SequencesShukla
- Pathogenic BRCA1 Mutations Disrupt Allosteric Control by BARD1Bowman
- Cryo-EM structures of ρ1 GABA(A) receptors with antagonist and agonist drugsLindahl
- Cryo-EM ligand building using AlphaFold3-like model and molecular dynamicsLindahl
- A Structure-Based Computational Pipeline for Broad-Spectrum Antiviral DiscoveryChodera
- Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0]Voelz
- Model Selection Using Replica Averaging with Bayesian Inference of Conformational PopulationsVoelz
- High-Resolution Tuning of Non-Natural and Cyclic Peptide Folding Landscapes against NMR Measurements Using Markov Models and Bayesian Inference of Conformational PopulationsVoelz
- Simple Method to Optimize the Spacing and Number of Alchemical Intermediates in Expanded Ensemble Free Energy CalculationsVoelz
- Automatic Forward Model Parameterization with Bayesian Inference of Conformational PopulationsVoelz
- Mechanistic basis for enhanced strigolactone sensitivity in KAI2 triple mutantShukla
- Multiple modes of cholesterol translocation in the human Smoothened receptorShukla
- BRCA1 in breast cancerBowman
- Resolving the conformational ensemble of a membrane protein by integrating small-angle scattering with AlphaFoldLindahl
- Engineering cardiolipin binding to an artificial membrane protein reveals determinants for lipid-mediated stabilizationLindahl
- SWEET Family Transporters Act as Water-Conducting Carrier Proteins in PlantsShukla
- Discovering cryptic pocket opening and binding of a stimulant derivative in a vestibular site of the 5-HT(3A) receptorLindahl
- The need to implement FAIR principles in biomolecular simulationsBowman
- Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v0.1]Voelz
- Prospective Evaluation of Structure-Based Simulations Reveal Their Ability to Predict the Impact of Kinase Mutations on Inhibitor BindingChodera
- Expanded ensemble predictions of toluene-water partition coefficients in the SAMPL9 log P challengeVoelz
- Substrate interactions guide cyclase engineering and lasso peptide diversificationShukla
- Rapid and accurate prediction of protein homo-oligomer symmetry using Seq2SymmBowman
- Molecular insights into the elevator-type mechanism of the cyanobacterial bicarbonate transporter BicAShukla
- Regulating IL-2 Immune Signaling Function Via A Core Allosteric Structural NetworkBowman
- Adaptive sampling-based structural prediction reveals opening of a GABA(A) receptor through the αβ interfaceLindahl
- Fine-tuning molecular mechanics force fields to experimental free energy measurementsChodera
2024
TitleGroup
- Energetics of substrate transport in proton-dependent oligopeptide transportersShukla
- An allosteric glueBowman
- Accounting for Fast vs Slow Exchange in Single Molecule FRET Experiments Reveals Hidden Conformational StatesBowman
- Benchmarking Cross-Docking Strategies in Kinase Drug DiscoveryChodera
- The G protein inhibitor YM-254890 is an allosteric glueBowman
- Improved Estimates of Folding Stabilities and Kinetics with Multiensemble Markov ModelsVoelz
- Dynamic Mechanism for Subtype Selectivity of EndocannabinoidsShukla
- Non-Markovian Dynamic Models Identify Non-Canonical KRAS-VHL Encounter Complex Conformations for Novel PROTAC DesignHuang
- Symmetry-adapted Markov state models of closing, opening, and desensitizing in α 7 nicotinic acetylcholine receptorsLindahl
- Nutmeg and SPICE: Models and Data for Biomolecular Machine LearningChodera
- Predicting drugs’ lipophilicity with Folding@homeVoelz
- Cyclopamine modulates smoothened receptor activity in a binding position dependent mannerShukla
- Lessons learned during the journey of data: from experiment to model for predicting kinase affinity, selectivity, polypharmacology, and resistanceChodera
- Divergent mechanisms of steroid inhibition in the human ρ1 GABA(A) receptorLindahl
- Stabilization of interdomain closure by a G protein inhibitorBowman
- Machine-learned molecular mechanics force fields from large-scale quantum chemical dataChodera
- AlphaFold and Protein Folding: Not Dead Yet! The Frontier Is Conformational EnsemblesBowman
- SGLT2 inhibitors activate pantothenate kinase in the human heartBowman
- Improving protein design on Folding@homeBowman
- Tackling CondensatesBowman
- Simulating the Skin Permeation Process of Ionizable MoleculesLindahl
- SWEET family transporters act as water conducting carrier proteins in plantsShukla
- The Arabidopsis AtSWEET13 transporter discriminates sugars by selective facial and positional substrate recognitionShukla
- Interplay between phosphorylation and oligomerization tunes the conformational ensemble of SWEET transportersShukla
- Connecting with single molecule experimentsBowman
- DrugGym: A testbed for the economics of autonomous drug discoveryChodera
- Functional and structural insights into activation of TRPV2 by weak acidsLindahl
- Allosteric Cholesterol Site in Glycine Receptors Characterized through Molecular SimulationsLindahl
- EspalomaCharge: Machine Learning-Enabled Ultrafast Partial Charge AssignmentChodera
- How does ApoE cause Alzheimer’s disease?Bowman
- Leveraging machine learning models for peptide-protein interaction predictionShukla
- G Protein Activation Occurs via a Largely Universal MechanismBowman
- Submillisecond Atomistic Molecular Dynamics Simulations Reveal Hydrogen Bond-Driven Diffusion of a Guest Peptide in Protein-RNA CondensateHuang
- Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network PotentialsChodera
- Toward physics-based precision medicine: Exploiting protein dynamics to design new therapeutics and interpret variantsBowman
- Functional regulation of aquaporin dynamics by lipid bilayer compositionShukla
- Homologous mutations in human β, embryonic, and perinatal muscle myosins have divergent effects on molecular power generationBowman
- PopShift: A Thermodynamically Sound Approach to Estimate Binding Free Energies by Accounting for Ligand-Induced Population Shifts from a Ligand-Free Markov State ModelBowman
- Binding Position Dependent Modulation of Smoothened Activity by CyclopamineShukla
- Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluidsLindahl
- Contribution of Signaling Partner Association to Strigolactone Receptor SelectivityShukla
- Drug Discovery in Low Data Regimes: Leveraging a Computational Pipeline for the Discovery of Novel SARS-CoV-2 Nsp14-MTase InhibitorsVoelz
- OpenMM 8: Molecular Dynamics Simulation with Machine Learning PotentialsChodera
2023
TitleGroup
- Adaptive Sampling Methods for Molecular Dynamics in the Era of Machine LearningShukla
- Markov State Model of Solvent Features Reveals Water Dynamics in Protein-Peptide BindingVoelz
- Expanded ensemble predictions of absolute binding free energies in the SAMPL9 host-guest challengeVoelz
- Death by a thousand cuts through kinase inhibitor combinations that maximize selectivity and enable rational multitargetingChodera
- Resolving binding pathways and solvation thermodynamics of plant hormone receptorsShukla
- Unraveling the Mystery of Drug Specificity: The Case of BlebbistatinBowman
- Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitorsBowman
- Unraveling the Secrets of G Protein Activation: A Molecular OdysseyBowman
- NNP/MM: Accelerating Molecular Dynamics Simulations with Machine Learning Potentials and Molecular MechanicsChodera
- Benchmarking Cross-Docking Strategies for Structure-Informed Machine Learning in Kinase Drug DiscoveryChodera
- Understanding Drug Skin Permeation Enhancers Using Molecular Dynamics SimulationsLindahl
- Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein ComplexChodera
- PopShift: A thermodynamically sound approach to estimate binding free energies by accounting for ligand-induced population shifts from a ligand-free MSMBowman
- Active Learning of the Conformational Ensemble of Proteins Using Maximum Entropy VAMPNetsShukla
- Folding@home: Achievements from over 20 years of citizen science herald the exascale eraBowman
- Accelerating Cryptic Pocket Discovery Using AlphaFoldBowman
- Functional Regulation of Aquaporin Dynamics by Lipid Bilayer CompositionShukla
- Automated simulation-based membrane protein refinement into cryo-EM dataLindahl
- Divergent Molecular Phenotypes in Point Mutations at the Same Residue in Beta-Myosin Heavy Chain Lead to Distinct CardiomyopathiesBowman
- Homologous mutations in β, embryonic, and perinatal muscle myosins have divergent effects on molecular power generationBowman
- Gentle and fast all-atom model refinement to cryo-EM densities via a maximum likelihood approachLindahl
- Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force FieldChodera
- The Effects of N-Linked Glycosylation on SLC6 TransportersShukla
- Distinct activation mechanisms regulate subtype selectivity of Cannabinoid receptorsShukla
- BICePs v2.0: Software for Ensemble Reweighting Using Bayesian Inference of Conformational PopulationsVoelz
- Remembering the Work of Phillip L. Geissler: A Coda to His Scientific TrajectoryBowman
- Effect of histidine covalent modification on strigolactone receptor activation and selectivityShukla
- Activation mechanism of the human Smoothened receptorShukla
- Structural Elucidation of Ivermectin Binding to α7nAChR and the Induced Channel DesensitizationLindahl
- Folding@home: achievements from over twenty years of citizen science herald the exascale eraBowman
- Turning high-throughput structural biology into predictive inhibitor designChodera
- Predicting locations of cryptic pockets from single protein structures using the PocketMiner graph neural networkBowman
- Reconciling membrane protein simulations with experimental DEER spectroscopy dataShukla
- Apolipoprotein E4 has extensive conformational heterogeneity in lipid-free and lipid-bound formsBowman
- Drug specificity and affinity are encoded in the probability of cryptic pocket opening in myosin motor domainsBowman
- SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning PotentialsChodera
- Discovery of a cryptic pocket in the AI-predicted structure of PPM1D phosphatase explains the binding site and potency of its allosteric inhibitorsBowman
2022
TitleGroup
- Biophysical characterization of calcium-binding and modulatory-domain dynamics in a pentameric ligand-gated ion channelLindahl
- Effects of Salinity and Temperature on the Flexibility and Function of a Polyextremophilic EnzymeVoelz
- Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at ScaleChodera
- Thirty years of molecular dynamics simulations on posttranslational modifications of proteinsShukla
- End-to-end differentiable construction of molecular mechanics force fieldsChodera
- Differential interactions of resting, activated, and desensitized states of the α7 nicotinic acetylcholine receptor with lipidic modulatorsLindahl
- Skin permeability prediction with MD simulation sampling spatial and alchemical reaction coordinatesLindahl
- Probing effects of the SARS-CoV-2 E protein on membrane curvature and intracellular calciumDelemotte
- Multiagent Reinforcement Learning-Based Adaptive Sampling for Conformational Dynamics of ProteinsShukla
- The nepenthesin insert in the Plasmodium falciparum aspartic protease plasmepsin V is necessary for enzyme functionBowman
- Oncogenic Mutations in the DNA-Binding Domain of FOXO1 that Disrupt Folding: Quantitative Insights from Experiments and Molecular SimulationsVoelz
- Structural and dynamic mechanisms of GABA(A) receptor modulators with opposing activitiesLindahl
- Open Force Field Evaluator: An Automated, Efficient, and Scalable Framework for the Estimation of Physical Properties from Molecular SimulationChodera
- Improving Force Field Accuracy by Training against Condensed-Phase Mixture PropertiesChodera
- Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use caseLindahl
- When SWEETs Turn Tweens: Updates and PerspectivesShukla
- Integration of machine learning with computational structural biology of plantsShukla
- A cryptic pocket in Ebola VP35 allosterically controls RNA bindingBowman
- Activation Mechanism of Strigolactone Receptors and Its Impact on Ligand Selectivity between Host and Parasitic PlantsShukla
- Estimation of binding rates and affinities from multiensemble Markov models and ligand decouplingVoelz
- Structural Rearrangement of the Serotonin Transporter Intracellular Gate Induced by Thr276 PhosphorylationShukla
- Mechanistic origin of partial agonism of tetrahydrocannabinol for cannabinoid receptorsShukla
- CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-findingChodera
- Dual Role of Strigolactone Receptor Signaling Partner in Inhibiting Substrate HydrolysisShukla
- Engineered ACE2 decoy mitigates lung injury and death induced by SARS-CoV-2 variantsShukla
- The substrate import mechanism of the human serotonin transporterShukla
- Bayesian-Inference-Driven Model Parametrization and Model Selection for 2CLJQ Fluid ModelsChodera
- Role of internal loop dynamics in antibiotic permeability of outer membrane porinsShukla
- Distinct Binding Mechanisms for Allosteric Sodium Ion in Cannabinoid ReceptorsShukla
- Unprotected peptide macrocyclization and stapling via a fluorine-thiol displacement reactionVoelz
- Molecular basis of the activation and dissociation of dimeric PYL2 receptor in abscisic acid signalingShukla
- Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [Article v0.1]Chodera
- Multiple conserved states characterize the twist landscape of the bacterial actin homolog MreBBowman
- Solution of the protein structure prediction problem at last: crucial innovations and next frontiersBowman
2021
TitleGroup
- Engineered High-Affinity ACE2 Peptide Mitigates ARDS and Death Induced by Multiple SARS-CoV-2 VariantsShukla
- Editorial: Experiments and Simulations: A Pas de Deux to Unravel Biological FunctionBowman
- Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sitesBowman
- Classic paper: Improved coarse-graining of Markov state models via explicit consideration of statistical uncertaintyBowman
- Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunityChodera
- Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escapeChodera
- What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding ModelsChodera
- Discovery of SARS-CoV-2 main protease inhibitors using a synthesis-directed de novo design modelChodera
- SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escapeChodera
- Best Practices for Alchemical Free Energy Calculations [Article v1.0]Chodera
- INK4 tumor suppressor proteins mediate resistance to CDK4/6 kinase inhibitorsChodera
- Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force FieldChodera
- Fitting quantum machine learning potentials to experimental free energy data: predicting tautomer ratios in solutionChodera
- Automated high throughput pKa and distribution coefficient measurements of pharmaceutical compounds for the SAMPL8 blind prediction challengeChodera
- Mutation in Abl kinase with altered drug-binding kinetics indicates a novel mechanism of imatinib resistanceChodera
- Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programsChodera
- Exploring zipping and assembly as a protein folding principleVoelz
- The protein folding problem: when will it be solved?Voelz
- Predicting peptide structures in native proteins from physical simulations of fragmentsVoelz
- Probing the nanosecond dynamics of a designed three-stranded beta-sheet with a massively parallel molecular dynamics simulationPande
- Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)Pande
- Unfolded-state dynamics and structure of protein L characterized by simulation and experimentPande
- Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBERVoelz
- De novo structure prediction and experimental characterization of folded peptoid oligomersVoelz
- Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulationsVoelz
- Computational screening and selection of cyclic peptide hairpin mimetics by molecular simulation and kinetic network modelsVoelz
- Bayesian inference of conformational state populations from computational models and sparse experimental observablesVoelz
- Molecular Simulation of Conformational Pre-Organization in Cyclic RGD PeptidesVoelz
- Microsecond simulations of mdm2 and its complex with p53 yield insight into force field accuracy and conformational dynamicsVoelz
- Using Kinetic Network Models To Probe Non-Native Salt-Bridge Effects on α-Helix FoldingVoelz
- Simulations of the regulatory ACT domain of human phenylalanine hydroxylase (PAH) unveil its mechanism of phenylalanine bindingVoelz
- Exposing the Nucleation Site in α-Helix Folding: A Joint Experimental and Simulation StudyVoelz
- Site-Specific Immuno-PET Tracer to Image PD-L1Voelz
- Reconciling Simulated Ensembles of Apomyoglobin with Experimental Hydrogen/Deuterium Exchange Data Using Bayesian Inference and Multiensemble Markov State ModelsVoelz
- Metal-Binding Q-Proline MacrocyclesVoelz
- A tutorial on building markov state models with MSMBuilder and coarse-graining them with BACEBowman
- Software for building Markov state modelsBowman
- An overview and practical guide to building Markov state modelsBowman
- Markov State Models to Elucidate Ligand Binding MechanismVoelz
- Introduction and overview of this bookPande
- Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathwaysPande
- Extensive conformational heterogeneity within protein coresBowman
- Fluctuations within folded proteins: implications for thermodynamic and allosteric regulationBowman
- Discovery of multiple hidden allosteric sites by combining Markov state models and experimentsBowman
- Accurately modeling nanosecond protein dynamics requires at least microseconds of simulationBowman
- Choice of Adaptive Sampling Strategy Impacts State Discovery, Transition Probabilities, and the Apparent Mechanism of Conformational ChangesBowman
- Solution-State Preorganization of Cyclic β-Hairpin Ligands Determines Binding Mechanism and Affinities for MDM2Voelz
- Reconciling Simulations and Experiments With BICePs: A ReviewVoelz
- Metal Cation-Binding Mechanisms of Q-Proline Peptoid Macrocycles in SolutionVoelz
- Assigning confidence to molecular property predictionVoelz
- Stacking Gaussian processes to improve [Formula: see text] predictions in the SAMPL7 challengeVoelz
- Expanded Ensemble Methods Can be Used to Accurately Predict Protein-Ligand Relative Binding Free EnergiesVoelz
- Antagonism between substitutions in β-lactamase explains a path not taken in the evolution of bacterial drug resistanceBowman
- SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the ProteomeBowman
- Computing and optimizing over all fixed-points of discrete systems on large networksBowman
- Protein sequence models for prediction and comparative analysis of the SARS-CoV-2 -human interactomeBowman
- The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNABowman
- Deep learning the structural determinants of protein biochemical properties by comparing structural ensembles with DiffNetsBowman
- SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteomeBowman
- Naturally Occurring Genetic Variants in the Oxytocin Receptor Alter Receptor Signaling ProfilesBowman
- Opening of a cryptic pocket in β-lactamase increases penicillinase activityBowman
- Protein folded states are kinetic hubsPande
- Everything you wanted to know about Markov State Models but were afraid to askBowman
- Taming the complexity of protein foldingPande
- Atomistic folding simulations of the five-helix bundle protein lambda(685)Pande
- Simple theory of protein folding kineticsPande
- Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experimentsPande
- Markov state model reveals folding and functional dynamics in ultra-long MD trajectoriesPande
- Calculation of rate spectra from noisy time series dataPande
- Characterization and rapid sampling of protein folding Markov state model topologiesPande
- Protein folding is mechanistically robustPande
- Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experimentPande
- Simple few-state models reveal hidden complexity in protein foldingPande
- Eigenvalues of the homogeneous finite linear one step master equation: applications to downhill foldingPande
- To milliseconds and beyond: challenges in the simulation of protein foldingPande
- Derivation and assessment of phase-shifted, disordered vector field models for frustrated solvent interactionsPande
- Emergence of glass-like behavior in Markov state models of protein folding dynamicsPande
- Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9Pande
- Inclusion of persistence length-based secondary structure in replica field theoretic models of heteropolymer freezingPande
- Probing the origins of two-state foldingPande
- Chemical kinetics and mechanisms of complex systems: a perspective on recent theoretical advancesPande
- Understanding protein folding using Markov state modelsPande
- A molecular interpretation of 2D IR protein folding experiments with Markov state modelsPande
- Statistical model selection for Markov models of biomolecular dynamicsPande
- Dynamical phase transitions reveal amyloid-like states on protein folding landscapesPande
- Complex pathways in folding of protein G explored by simulation and experimentPande
- Perspective: Markov models for long-timescale biomolecular dynamicsPande
- Markov state models provide insights into dynamic modulation of protein functionPande
- The dynamic conformational cycle of the group I chaperonin C-termini revealed via molecular dynamics simulationPande
- Percolation-like phase transitions in network models of protein dynamicsPande
- Free energy landscape of activation in a signalling protein at atomic resolutionPande
- A network of molecular switches controls the activation of the two-component response regulator NtrCPande
- Efficient maximum likelihood parameterization of continuous-time Markov processesPande
- Modeling molecular kinetics with tICA and the kernel trickPande
- Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational DynamicsPande
- Conformational heterogeneity of the calmodulin binding interfacePande
- Markov State Models and tICA Reveal a Nonnative Folding Nucleus in Simulations of NuG2Pande
- Finding Our Way in the Dark ProteomePande
- Optimized parameter selection reveals trends in Markov state models for protein foldingPande
- MSMBuilder: Statistical Models for Biomolecular DynamicsPande
- Identification of simple reaction coordinates from complex dynamicsPande
- Ward Clustering Improves Cross-Validated Markov State Models of Protein FoldingPande
- Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheYPande
- Modeling the mechanism of CLN025 beta-hairpin formationPande
- A Minimum Variance Clustering Approach Produces Robust and Interpretable Coarse-Grained ModelsPande
- Markov State Models: From an Art to a SciencePande
- Solving the RNA design problem with reinforcement learningPande
- Variational encoding of complex dynamicsPande
- Markov state modeling of membrane transport proteinsShukla
- Markov state models of proton- and pore-dependent activation in a pentameric ligand-gated ion channelLindahl
- Role of substrate recognition in modulating strigolactone receptor selectivity in witchweedShukla
- Probing solution structure of the pentameric ligand-gated ion channel GLIC by small-angle neutron scatteringLindahl
- Impact of Increased Membrane Realism on Conformational Sampling of ProteinsShukla
- How do antiporters exchange substrates across the cell membrane? An atomic-level description of the complete exchange cycle in NarKShukla
- Regulation of a pentameric ligand-gated ion channel by a semiconserved cationic lipid-binding siteLindahl
- Dynamic closed states of a ligand-gated ion channel captured by cryo-EM and simulationsLindahl
- SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potentialBowman
- A comprehensive mechanism for 5-carboxylcytosine-induced transcriptional pausing revealed by Markov state modelsHuang
- Molecular Reorganization during the Formation of the Human Skin Barrier Studied In SituLindahl
- Overview of the SAMPL6 pKa challenge: evaluating small molecule microscopic and macroscopic pKa predictionsChodera
2020
TitleGroup
- Is Structure-Based Drug Design Ready for Selectivity Optimization?Chodera
- An angular motion of a conserved four-helix bundle facilitates alternating access transport in the TtNapA and EcNhaA transportersLindahl
- SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potentialBowman
- Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACSLindahl
- Shared structural mechanisms of general anaesthetics and benzodiazepinesLindahl
- Improvement in ADMET Prediction with Multitask Deep FeaturizationPande
- Machine Learning Force Fields and Coarse-Grained Variables in Molecular Dynamics: Application to Materials and Biological SystemsChodera
- Computational Studies of SARS-CoV-2 3CLpro: Insights from MD SimulationsLindahl
- Citizen Scientists Create an Exascale Computer to Combat COVID-19Bowman
- Conformational distributions of isolated myosin motor domains encode their mechanochemical propertiesBowman
- The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculationsChodera
- Standard state free energies, not pK(a)s, are ideal for describing small molecule protonation and tautomeric statesChodera
- Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challengeChodera
- Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P ChallengeChodera
- Investigating Cryptic Binding Sites by Molecular Dynamics SimulationsBowman
- Dynamical model of the CLC-2 ion channel reveals conformational changes associated with selectivity-filter gatingPande
- Microcanonical coarse-graining of the kinetic Ising modelVoelz
- Divalent cations promote TALE DNA-binding specificityShukla
- Structural Consequences of Multisite Phosphorylation in the BAK1 Kinase DomainShukla
- Spatial and temporal alterations in protein structure by EGF regulate cryptic cysteine oxidationBowman
- Molecular Mechanism of Brassinosteroid Perception by the Plant Growth Receptor BRI1Shukla
- Adaptive Markov state model estimation using short reseeding trajectoriesVoelz
2019
TitleGroup
- Binding Thermodynamics of Host-Guest Systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field InitiativeChodera
- Agonist Selectivity and Ion Permeation in the α3β4 Ganglionic Nicotinic ReceptorLindahl
- Distinct Substrate Transport Mechanism Identified in Homologous Sugar TransportersShukla
- eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spacesLindahl
- Molecular Basis of the Glucose Transport Mechanism in PlantsShukla
- Dodine as a Kosmo-Chaotropic AgentShukla
- Oncogenic mutations at the EGFR ectodomain structurally converge to remove a steric hindrance on a kinase-coupled cryptic epitopeLindahl
- The dynamic conformational landscape of the protein methyltransferase SETD8Chodera
- Dewetting Controls Plant Hormone Perception and Initiation of Drought Resistance SignalingShukla
- Advanced Methods for Accessing Protein Shape-Shifting Present New Therapeutic OpportunitiesBowman
- What Makes a Kinase Promiscuous for Inhibitors?Chodera
- Cooperative Changes in Solvent Exposure Identify Cryptic Pockets, Switches, and Allosteric CouplingBowman
- Fluorinated Aromatic Monomers as Building Blocks To Control α-Peptoid Conformation and StructureVoelz
- Synthesis of spiro-2,6-dioxopiperazine and spiro-2,6-dioxopyrazine scaffolds using amino acids in a three-component reaction to generate potential Sigma-1 (σ(1)) receptor selective ligandsPande
- OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. BasicsChodera
- OpenPathSampling: A Python Framework for Path Sampling Simulations. 2. Building and Customizing Path Ensembles and Sample SchemesChodera
- Enspara: Modeling molecular ensembles with scalable data structures and parallel computingBowman
- Toward Learned Chemical Perception of Force Field Typing RulesChodera
- Intradomain Interactions in an NMDA Receptor Fragment Mediate N-Glycan Processing and Conformational SamplingPande
- Ten simple rules on how to create open access and reproducible molecular simulations of biological systemsLindahl
2018
TitleGroup
- SAXS-guided Enhanced Unbiased Sampling for Structure Determination of Proteins and ComplexesShukla
- Note: Variational encoding of protein dynamics benefits from maximizing latent autocorrelationPande
- PotentialNet for Molecular Property PredictionPande
- Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular sciencePande
- Escaping Atom Types in Force Fields Using Direct Chemical PerceptionChodera
- Allosteric potentiation of a ligand-gated ion channel is mediated by access to a deep membrane-facing cavityLindahl
- Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbindingBowman
- pK(a) measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragmentsChodera
- Overview of the SAMPL6 host-guest binding affinity prediction challengeChodera
- Free Energy Landscape of the Complete Transport Cycle in a Key Bacterial TransporterShukla
- Uptake dynamics in the Lactose permease (LacY) membrane protein transporterLindahl
- Automated design of collective variables using supervised machine learningPande
- Computer Simulations Predict High Structural Heterogeneity of Functional State of NMDA ReceptorsPande
- Towards simple kinetic models of functional dynamics for a kinase subfamilyPande
- Predicting drug permeability through skin using molecular dynamics simulationLindahl
- An Open Library of Human Kinase Domain Constructs for Automated Bacterial ExpressionChodera
- Human skin barrier structure and function analyzed by cryo-EM and molecular dynamics simulationLindahl
- Elucidating the inhibition of peptidoglycan biosynthesis in Staphylococcus aureus by albocycline, a macrolactone isolated from Streptomyces maizeusVoelz
- Transfer Learning from Markov Models Leads to Efficient Sampling of Related SystemsPande
- Model Selection Using BICePs: A Bayesian Approach for Force Field Validation and ParameterizationVoelz
- Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte CarloChodera
- Biomolecular Simulations under Realistic Macroscopic Salt ConditionsChodera
- Human skin barrier formation takes place via a cubic to lamellar lipid phase transition as analyzed by cryo-electron microscopy and EM-simulationLindahl
- Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular SystemsChodera
- Communication: Adaptive boundaries in multiscale simulationsPande
- Structural Transitions in Ceramide Cubic Phases during Formation of the Human Skin BarrierLindahl
- Transferable neural networks for enhanced sampling of protein dynamics.Pande
- Universality of the Sodium Ion Binding Mechanism in Class A G-Protein-Coupled ReceptorsShukla
- Using molecular simulation to explore the nanoscale dynamics of the plant kinomeShukla
- A dynamic mechanism for allosteric activation of Aurora kinase A by activation loop phosphorylationChodera
- Theoretical restrictions on longest implicit time scales in Markov state models of biomolecular dynamicsPande
- Characterizing Conformational Dynamics of Proteins Using Evolutionary CouplingsShukla
- REDOR NMR Reveals Multiple Conformers for a Protein Kinase C Ligand in a Membrane EnvironmentPande
- Markov State Models: From an Art to a Science.Pande
- Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculationsChodera
- Bayesian analysis of isothermal titration calorimetry for binding thermodynamicsChodera
2017
TitleGroup
- Prediction of New Stabilizing Mutations Based on Mechanistic Insights from Markov State ModelsBowman
- Allosteric Control of a Plant Receptor Kinase through S-GlutathionylationShukla
- Control of porphyrin interactions via structural changes of a peptoid scaffold.Voelz
- Solution-Phase Conformation and Dynamics of Conjugated Isoindigo-Based Donor-Acceptor Polymer Single ChainsPande
- Bladder-cancer-associated mutations in RXRA activate peroxisome proliferator-activated receptors to drive urothelial proliferationBowman
- Millisecond dynamics of BTK reveal kinome-wide conformational plasticity within the apo kinase domainPande
- Simulated Dynamics of Glycans on Ligand-Binding Domain of NMDA Receptors Reveals Strong Dynamic Coupling between Glycans and Protein CorePande
- Note: MSM lag time cannot be used for variational model selectionPande
- Predicting Optimal DEER Label Positions to Study Protein Conformational HeterogeneityShukla
- Enhanced unbiased sampling of protein dynamics using evolutionary coupling informationShukla
- A drug pocket at the lipid bilayer-potassium channel interfaceLindahl
- Bridging Microscopic and Macroscopic Mechanisms of p53-MDM2 Binding with Kinetic Network ModelsVoelz
- Molecular dynamics simulations reveal the conformational dynamics of Arabidopsis thaliana BRI1 and BAK1 receptor-like kinasesShukla
- Molecular simulations and free-energy calculations suggest conformation-dependent anion binding to a cytoplasmic site as a mechanism for Na(+)/K(+)-ATPase ion selectivityVoelz
- Computational and Experimental Evaluation of Designed β-Cap Hairpins Using Molecular Simulations and Kinetic Network ModelsVoelz
- Is Multitask Deep Learning Practical for Pharma?Pande
- OpenMM 7: Rapid development of high performance algorithms for molecular dynamicsChodera
- tICA-Metadynamics: Accelerating Metadynamics by Using Kinetically Selected Collective VariablesPande
- Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv databaseChodera
- Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15Pande
- Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing unitsPande
- Quantifying Allosteric Communication via Both Concerted Structural Changes and Conformational Disorder with CARDSBowman
- Computationally Discovered Potentiating Role of Glycans on NMDA ReceptorsPande
- Markov modeling reveals novel intracellular modulation of the human TREK-2 selectivity filterPande
- Propagation of the Allosteric Modulation Induced by Sodium in the δ-Opioid ReceptorBowman
- Molecular dynamics simulations reveal ligand-controlled positioning of a peripheral protein complex in membranesPande
- Discovery of novel brain permeable and G protein-biased beta-1 adrenergic receptor partial agonists for the treatment of neurocognitive disordersPande
- Application of Hidden Markov Models in Biomolecular SimulationsShukla
- Warfarin traps human vitamin K epoxide reductase in an intermediate state during electron transferBowman
- Designing small molecules to target cryptic pockets yields both positive and negative allosteric modulatorsBowman
2016
TitleGroup
- A Maximum-Caliber Approach to Predicting Perturbed Folding Kinetics Due to MutationsVoelz
- Training and Validation of a Liquid-Crystalline Phospholipid Bilayer Force Field.Pande
- Membrane Anchoring and Ion-Entry Dynamics in P-type ATPase Copper TransportLindahl
- Defining NADH-Driven Allostery Regulating Apoptosis-Inducing FactorBowman
- Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challengeChodera
- Allosteric binding site in a Cys-loop receptor ligand-binding domain unveiled in the crystal structure of ELIC in complex with chlorpromazineLindahl
- Modelling proteins' hidden conformations to predict antibiotic resistanceBowman
- Structure and Dynamics of PD-L1 and an Ultra-High-Affinity PD-1 Receptor MutantBowman
- Advanced Potential Energy Surfaces for Molecular SimulationPande
- Mechanistically distinct cancer-associated mTOR activation clusters predict sensitivity to rapamycin.Chodera
- Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulationsLindahl
- Markov models of the apo-MDM2 lid region reveal diffuse yet two-state binding dynamics and receptor poses for computational dockingVoelz
- Transition path theory analysis of c-Src kinase activationPande
- Tungstate as a Transition State Analog for Catalysis by Alkaline PhosphatasePande
- Reciprocal voltage sensor-to-pore coupling leads to potassium channel C-type inactivationLindahl
- Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily ScaleChodera
- Discovery of a regioselectivity switch in nitrating P450s guided by molecular dynamics simulations and Markov modelsPande
- A Simple Method for Automated Equilibration Detection in Molecular SimulationsChodera
- CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force FieldPande
- The Molecular Basis of Polyunsaturated Fatty Acid Interactions with the Shaker Voltage-Gated Potassium ChannelLindahl
- How to Run FAST SimulationsBowman
2015
TitleGroup
- Insights into Peptoid Helix Folding Cooperativity from an Improved Backbone PotentialVoelz
- Direct-Space Corrections Enable Fast and Accurate Lorentz-Berthelot Combination Rule Lennard-Jones Lattice SummationLindahl
- FAST Conformational Searches by Balancing Exploration/Exploitation Trade-OffsBowman
- Modeling error in experimental assays using the bootstrap principle: understanding discrepancies between assays using different dispensing technologiesChodera
- MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics TrajectoriesPande
- Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data ArchiveChodera
- Conformational gating dynamics in the GluCl anion-selective chloride channelLindahl
- Heat dissipation guides activation in signaling proteinsPande
- Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water ModelPande
- SAXS-Guided MetadynamicsLindahl
- United polarizable multipole water model for molecular mechanics simulationPande
- OpenMM: A Hardware Independent Framework for Molecular SimulationsPande
- Potential-based dynamical reweighting for Markov state models of protein dynamicsPande
- Molecular simulation workflows as parallel algorithms: the execution engine of Copernicus, a distributed high-performance computing platformLindahl
- Kinetic network models of tryptophan mutations in β-hairpins reveal the importance of non-native interactionsVoelz
- Variational cross-validation of slow dynamical modes in molecular kineticsPande
- Conserve Water: A Method for the Analysis of Solvent in Molecular DynamicsPande
- Entropy-production-driven oscillators in simple nonequilibrium networksPande
- Cloud computing approaches for prediction of ligand binding poses and pathwaysPande
- Coupled diffusion in lipid bilayers upon close approachLindahl
- Elucidating Ligand-Modulated Conformational Landscape of GPCRs Using Cloud-Computing ApproachesPande
- Molecular dynamics simulationsLindahl
2014
TitleGroup
- Automatic Selection of Order Parameters in the Analysis of Large Scale Molecular Dynamics SimulationsPande
- Surprisal Metrics for Quantifying Perturbed Conformational Dynamics in Markov State ModelsVoelz
- Discovering chemistry with an ab initio nanoreactorPande
- Building Force Fields: An Automatic, Systematic, and Reproducible ApproachPande
- Markov state models of biomolecular conformational dynamicsChodera
- Bayesian energy landscape tilting: towards concordant models of molecular ensemblesPande
- Activation pathway of Src kinase reveals intermediate states as targets for drug designShukla
- Spectral Rate Theory for Two-State KineticsChodera
- SCISSORS: practical considerationsPande
2013
TitleGroup
- Finite domain simulations with adaptive boundaries: accurate potentials and nonequilibrium movesetsPande
- Calculations of the electric fields in liquid solutionsPande
- MSMExplorer: Visualizing Markov State Models for Biomolecule Folding Simulations.Pande
- Association dynamics and linear and nonlinear optical properties of an N-acetylaladanamide probe in a POPC membraneLindahl
- Systematic improvement of a classical molecular model of waterPande
- Long Timestep Molecular Dynamics on the Graphical Processing UnitPande
- Lennard-Jones Lattice Summation in Bilayer Simulations Has Critical Effects on Surface Tension and Lipid PropertiesLindahl
- Inhibition versus potentiation of ligand-gated ion channels can be altered by a single mutation that moves ligands between intra- and intersubunit sitesLindahl
- Stabilization of the GluCl ligand-gated ion channel in the presence and absence of ivermectinLindahl
- Functional understanding of solvent structure in GroEL cavity through dipole field analysisPande
- GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkitLindahl
- OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular SimulationPande
- The conserved phenylalanine in the K+ channel voltage-sensor domain creates a barrier with unidirectional effectsLindahl
- Building Markov state models with solvent dynamicsPande
- Molecular dynamics simulations for the ranking, evaluation, and refinement of computationally designed proteinsPande
- Persistent topology and metastable state in conformational dynamicsPande
- SWEETLEAD: an in silico database of approved drugs, regulated chemicals, and herbal isolates for computer-aided drug discoveryPande
- Inferring the rate-length law of protein foldingPande
- Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and designChodera
2012
TitleGroup
- Reducing the effect of Metropolization on mixing times in molecular dynamics simulationsPande
- Effects of familial mutations on the monomer structure of Aβ₄₂Pande
- Mechanistic and structural insight into the functional dichotomy between IL-2 and IL-15Pande
- A simple model predicts experimental folding rates and a hub-like topologyPande
- Design of β-amyloid aggregation inhibitors from a predicted structural motifPande
- Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR MeasurementsPande
- Simbios: an NIH national center for physics-based simulation of biological structuresPande
- Exploiting a natural conformational switch to engineer an interleukin-2 'superkine'Pande
- Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomerPande
- A-site residues move independently from P-site residues in all-atom molecular dynamics simulations of the 70S bacterial ribosomePande
- Sequence coevolution between RNA and protein characterized by mutual information between residue tripletsPande
- Molecular mechanism for the dual alcohol modulation of Cys-loop receptorsLindahl
2011
TitleGroup
- Copernicus: A new paradigm for parallel adaptive molecular dynamics.Lindahl
- MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond ScalePande
- Error bounds on the SCISSORS approximation methodPande
- Anatomy of high-performance 2D similarity calculationsPande
- CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithmsPande
- A smoothly decoupled particle interface: new methods for coupling explicit and implicit solventPande
- Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydrationPande
- 3₁₀-helix conformation facilitates the transition of a voltage sensor S4 segment toward the down stateLindahl
- Calculation of local water densities in biological systems: a comparison of molecular dynamics simulations and the 3D-RISM-KH molecular theory of solvationPande
- Rationally designed turn promoting mutation in the amyloid-β peptide sequence stabilizes oligomers in solutionPande
2010
TitleGroup
- A high-performance parallel-generalized Born implementation enabled by tabulated interaction rescalingLindahl
- Speeding development and execution speed with Just In Time GPU code development approaches.Pande
- Large-scale Chemical Informatics on the GPU.Pande
- Hard Data on Soft Errors: A Large-Scale Assessment of Real-World Error Rates in GPGPU.Pande
- OpenMM: A Hardware Abstraction Layer for Molecular Simulations.Pande
- Current Status of the AMOEBA Polarizable Force Field.Chodera
- Water Ordering at Membrane Interfaces Controls Fusion DynamicsPande
- Non-bulk-like solvent behavior in the ribosome exit tunnelPande
- Bayesian inference for Brownian dynamicsPande
- SCISSORS: a linear-algebraical technique to rapidly approximate chemical similaritiesPande
- Atomic-resolution simulations predict a transition state for vesicle fusion defined by contact of a few lipid tailsPande
- Polarizable atomic multipole x-ray refinement: hydration geometry and application to macromoleculesPande
- Network models for molecular kinetics and their initial applications to human healthPande
- Efficient nonbonded interactions for molecular dynamics on a graphics processing unitPande
- SIML: a fast SIMD algorithm for calculating LINGO chemical similarities on GPUs and CPUsPande
- Charge, hydrophobicity, and confined water: putting past simulations into a simple theoretical frameworkPande
- CCMA: A Robust, Parallelizable Constraint Method for Molecular SimulationsPande
- Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water ModelsLindahl
- PAPER--accelerating parallel evaluations of ROCSPande
- Bayesian detection of intensity changes in single molecule and molecular dynamics trajectoriesPande
- "Cross-graining": efficient multi-scale simulation via Markov state modelsPande
- Enhanced modeling via network theory: Adaptive sampling of Markov state modelsPande
- Constructing multi-resolution Markov State Models (MSMs) to elucidate RNA hairpin folding mechanismsHuang
2009
TitleGroup
- Do conformational biases of simple helical junctions influence RNA folding stability and specificity?Pande
- Rapid equilibrium sampling initiated from nonequilibrium dataPande
- Bayesian comparison of Markov models of molecular dynamics with detailed balance constraintPande
- Folding@home: lessons from eight years of distributed computing.Pande
- The Fip35 WW Domain Folds with Structural and Mechanistic Heterogeneity in Molecular Dynamics Simulations.Pande
- Using generalized ensemble simulations and Markov state models to identify conformational statesPande
- Progress and challenges in the automated construction of Markov state models for full protein systemsPande
- Protein contents in biological membranes can explain abnormal solvation of charged and polar residuesLindahl
- Bayesian single-exponential kinetics in single-molecule experiments and simulationsPande
- Polarizable atomic multipole X-ray refinement: application to peptide crystalsPande
- Combining molecular dynamics with bayesian analysis to predict and evaluate ligand-binding mutations in influenza hemagglutininPande
- The roles of entropy and kinetics in structure predictionPande
- The predicted structure of the headpiece of the Huntingtin protein and its implications on Huntingtin aggregationPande
- The role of lipid composition for insertion and stabilization of amino acids in membranesLindahl
- Accelerating molecular dynamic simulation on graphics processing unitsPande
- Topological methods for exploring low-density states in biomolecular folding pathwaysPande
- Simulated tempering yields insight into the low-resolution Rosetta scoring functionsPande
- Conformational changes and slow dynamics through microsecond polarized atomistic molecular simulation of an integral Kv1.2 ion channelLindahl
- Accelerating molecular dynamic simulation on the cell processor and Playstation 3Pande
- Titratable amino acid solvation in lipid membranes as a function of protonation stateLindahl
- A multiscale approach to sampling nascent peptide chains in the ribosomal exit tunnelPande
- Combining mutual information with structural analysis to screen for functionally important residues in influenza hemagglutininPande
2008
TitleGroup
- Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approachPande
- Side-chain recognition and gating in the ribosome exit tunnelPande
- Potential for modulation of the hydrophobic effect inside chaperoninsPande
- Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemblePande
- Chemical denaturants inhibit the onset of dewettingPande
- A role for confined water in chaperonin functionPande
- The Simbios National Center: Systems Biology in MotionPande
- Membrane proteins: molecular dynamics simulationsLindahl
- Structural insight into RNA hairpin folding intermediatesPande
- Using multiple templates to improve quality of homology models in automated homology modelingLindahl
- Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environmentPande
- Prediction of membrane-protein topology from first principlesLindahl
- Solvent viscosity dependence of the protein folding dynamicsPande
- Effects of long-range electrostatic forces on simulated protein folding kineticsPande
- Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulationsLindahl
- GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular SimulationLindahl
- Theory for an order-driven disruption of the liquid state in waterPande
- Molecular dynamics simulationsLindahl
2007
TitleGroup
- Folding and misfolding of the collagen triple helix: Markov analysis of molecular dynamics simulationsPande
- Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiecePande
- Control of membrane fusion mechanism by lipid composition: predictions from ensemble molecular dynamicsPande
- Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics.Pande
- Storage@home: Petascale Distributed StoragePande
- Persistent voids: a new structural metric for membrane fusionPande
- Choosing weights for simulated temperingPande
- Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamicsPande
- Protein folding under confinement: a role for solventPande
- Local structure formation in simulations of two small proteinsPande
- Predicting structure and dynamics of loosely-ordered protein complexes: influenza hemagglutinin fusion peptidePande
2006
TitleGroup
- Amino-acid solvation structure in transmembrane helices from molecular dynamics simulationsLindahl
- Bayesian update method for adaptive weighted samplingPande
- N-Body simulation on GPUsPande
- Folding Simulations of the Villin Headpiece in All-Atom Detail.Pande
- On the role of chemical detail in simulating protein folding kinetics.Pande
- Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamicsPande
- Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusionPande
- Electric fields at the active site of an enzyme: direct comparison of experiment with theoryPande
- Kinetic definition of protein folding transition state ensembles and reaction coordinatesPande
- Nanotube confinement denatures protein helicesPande
- Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiecePande
- Kinetic computational alanine scanning: application to p53 oligomerizationPande
- Can conformational change be described by only a few normal modes?Pande
- The solvation interface is a determining factor in peptide conformational preferencesPande
- Validation of Markov state models using Shannon's entropyPande
2005
TitleGroup
- A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptidesPande
- Error analysis and efficient sampling in Markovian state models for molecular dynamicsPande
- How large is alpha-helix in solution? Studies of the radii of gyration of helical peptides by SAXS and MD.Pande
- Direct calculation of the binding free energies of FKBP ligands using the Fujitsu BioServer massively parallel computer.Pande
- Unusual compactness of a polyproline type II structure.Pande
- Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and waterPande
- Foldamer dynamics expressed via Markov state models. II. State space decompositionPande
- Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scalingPande
- One-dimensional reaction coordinate and the corresponding potential of mean force from commitment probability distributionPande
- Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integrationPande
- Exploring the helix-coil transition via all-atom equilibrium ensemble simulationsPande
- Does water play a structural role in the folding of small nucleic acids?Pande
- Solvation free energies of amino acid side chain analogs for common molecular mechanics water modelsPande
- Length dependent folding kinetics of phenylacetylene oligomers: structural characterization of a kinetic trapPande
- Dimerization of the p53 oligomerization domain: identification of a folding nucleus by molecular dynamics simulationsPande
- How well can simulation predict protein folding kinetics and thermodynamics?Pande
2004
TitleGroup
- Foldamer simulations: novel computational methods and applications to poly-phenylacetylene oligomersPande
- How does averaging affect protein structure comparison on the ensemble level?Pande
- Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpinPande
- Molecular dynamics simulation of lipid reorientation at bilayer edgesPande
- Simulations of the role of water in the protein-folding mechanismPande
- Does native state topology determine the RNA folding mechanism?Pande
- Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopyPande
2003
TitleGroup
- Structural correspondence between the alpha-helix and the random-flight chain resolves how unfolded proteins can have native-like propertiesPande
- Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins.Pande
- Solvent Viscosity Dependence of the Folding Rate of a Small Protein: Distributed Computing Study.Pande
- Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methodsPande
- Sequence optimization for native state stability determines the evolution and folding kinetics of a small proteinPande
- Insights into nucleic acid conformational dynamics from massively parallel stochastic simulationsPande
- Increased detection of structural templates using alignments of designed sequencesPande
- Meeting halfway on the bridge between protein folding theory and experimentPande
- Molecular dynamics simulations of phospholipid bilayers with cholesterolLindahl
- Multiplexed-replica exchange molecular dynamics method for protein folding simulationPande
- Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computingPande
2002
TitleGroup
- The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulationsPande
- Thoroughly sampling sequence space: large-scale protein design of structural ensemblesPande
- Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computingPande
- Absolute comparison of simulated and experimental protein-folding dynamicsPande
- Native-like mean structure in the unfolded ensemble of small proteinsPande
- Folding@home and Genome@Home: Using distributed computing to tackle previously intractable problems in computational biology.Pande
- Atomistic protein folding simulations on the submillisecond timescale using worldwide distributed computing.Pande
- RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloopPande
2001
TitleGroup
2000
TitleGroup