Here are our peer-reviewed results from Folding@home. For summaries of these methods and papers, as well as the scientific background behind Folding@home, please see the Folding@home article on Wikipedia.

Note that it can take quite a while to go from a result to a published peer review article (often as much as a year). These papers represent our progress to date that’s publicly available, with lots more on the way.

The distribution rules for published papers vary by the publication in which the paper appears. Due to these rules, a public web-source of each paper may not be immediately available. If full version is not linked below or available elsewhere on the Internet (Google Scholar can be helpful for this), most, if not all of these publications are freely available at a local municipal or collegial library. These articles are written for scientists, so the contents are fairly technical.

2024

• Predicting drugs’ lipophilicity with Folding@home

• Improving protein design on Folding@home

• Tackling Condensates

• Connecting with single molecule experiments

• How does ApoE cause Alzheimer’s disease?

2023

• Unraveling the Mystery of Drug Specificity: The Case of Blebbistatin

• Unraveling the Secrets of G Protein Activation: A Molecular Odyssey

2022

• Unprotected peptide macrocyclization and stapling via a fluorine-thiol displacement reaction

• SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids

2021

• Editorial: Experiments and Simulations: A Pas de Deux to Unravel Biological Function

• Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites

• Classic paper: Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty

• Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

• Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape

• What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models

• Discovery of SARS-CoV-2 main protease inhibitors using a synthesis-directed de novo design model

• SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape

• Best Practices for Alchemical Free Energy Calculations [Article v1.0]

• INK4 tumor suppressor proteins mediate resistance to CDK4/6 kinase inhibitors

• Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field

• Fitting quantum machine learning potentials to experimental free energy data: predicting tautomer ratios in solution

• Automated high throughput pKa and distribution coefficient measurements of pharmaceutical compounds for the SAMPL8 blind prediction challenge

• Mutation in Abl kinase with altered drug-binding kinetics indicates a novel mechanism of imatinib resistance

• Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs

• Exploring zipping and assembly as a protein folding principle

• The protein folding problem: when will it be solved?

• Predicting peptide structures in native proteins from physical simulations of fragments

• Probing the nanosecond dynamics of a designed three-stranded beta-sheet with a massively parallel molecular dynamics simulation

• Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)

• Unfolded-state dynamics and structure of protein L characterized by simulation and experiment

• Atomistic folding simulations of the five-helix bundle protein λ(6−85)

• Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER

• De novo structure prediction and experimental characterization of folded peptoid oligomers

• Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations

• Computational screening and selection of cyclic peptide hairpin mimetics by molecular simulation and kinetic network models

• Bayesian inference of conformational state populations from computational models and sparse experimental observables

• Molecular Simulation of Conformational Pre-Organization in Cyclic RGD Peptides

• Microsecond simulations of mdm2 and its complex with p53 yield insight into force field accuracy and conformational dynamics

• Using Kinetic Network Models To Probe Non-Native Salt-Bridge Effects on α-Helix Folding

• Simulations of the regulatory ACT domain of human phenylalanine hydroxylase (PAH) unveil its mechanism of phenylalanine binding

• Exposing the Nucleation Site in α-Helix Folding: A Joint Experimental and Simulation Study

• Site-Specific Immuno-PET Tracer to Image PD-L1

• Reconciling Simulated Ensembles of Apomyoglobin with Experimental Hydrogen/Deuterium Exchange Data Using Bayesian Inference and Multiensemble Markov State Models

• Metal-Binding Q-Proline Macrocycles

• Software for building Markov state models

• Quantitative comparison of alternative methods for coarse-graining biological networks

• A tutorial on building markov state models with MSMBuilder and coarse-graining them with BACE

• Extensive conformational heterogeneity within protein cores

• Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

• Introduction and overview of this book

• Markov State Models to Elucidate Ligand Binding Mechanism

• An overview and practical guide to building Markov state models

• Accurately modeling nanosecond protein dynamics requires at least microseconds of simulation

• Discovery of multiple hidden allosteric sites by combining Markov state models and experiments

• Fluctuations within folded proteins: implications for thermodynamic and allosteric regulation

• Choice of Adaptive Sampling Strategy Impacts State Discovery, Transition Probabilities, and the Apparent Mechanism of Conformational Changes

• Solution-State Preorganization of Cyclic β-Hairpin Ligands Determines Binding Mechanism and Affinities for MDM2

• Reconciling Simulations and Experiments With BICePs: A Review

• Metal Cation-Binding Mechanisms of Q-Proline Peptoid Macrocycles in Solution

• Assigning confidence to molecular property prediction

• Stacking Gaussian processes to improve [Formula: see text] predictions in the SAMPL7 challenge

• Expanded Ensemble Methods Can be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies

• Antagonism between substitutions in β-lactamase explains a path not taken in the evolution of bacterial drug resistance

• SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome

• Computing and optimizing over all fixed-points of discrete systems on large networks

• Protein sequence models for prediction and comparative analysis of the SARS-CoV-2 -human interactome

• The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA

• Deep learning the structural determinants of protein biochemical properties by comparing structural ensembles with DiffNets

• SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome

• Naturally Occurring Genetic Variants in the Oxytocin Receptor Alter Receptor Signaling Profiles

• Opening of a cryptic pocket in β-lactamase increases penicillinase activity

• Protein folded states are kinetic hubs

• Everything you wanted to know about Markov State Models but were afraid to ask

• Taming the complexity of protein folding

• Atomistic folding simulations of the five-helix bundle protein lambda(685)

• Simple theory of protein folding kinetics

• Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments

• Markov state model reveals folding and functional dynamics in ultra-long MD trajectories

• Calculation of rate spectra from noisy time series data

• Characterization and rapid sampling of protein folding Markov state model topologies

• Protein folding is mechanistically robust

• Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment

• Simple few-state models reveal hidden complexity in protein folding

• Eigenvalues of the homogeneous finite linear one step master equation: applications to downhill folding

• To milliseconds and beyond: challenges in the simulation of protein folding

• Derivation and assessment of phase-shifted, disordered vector field models for frustrated solvent interactions

• Emergence of glass-like behavior in Markov state models of protein folding dynamics

• Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9

• Inclusion of persistence length-based secondary structure in replica field theoretic models of heteropolymer freezing

• Probing the origins of two-state folding

• Chemical kinetics and mechanisms of complex systems: a perspective on recent theoretical advances

• Understanding protein folding using Markov state models

• A molecular interpretation of 2D IR protein folding experiments with Markov state models

• Statistical model selection for Markov models of biomolecular dynamics

• Dynamical phase transitions reveal amyloid-like states on protein folding landscapes

• Complex pathways in folding of protein G explored by simulation and experiment

• Perspective: Markov models for long-timescale biomolecular dynamics

• Markov state models provide insights into dynamic modulation of protein function

• The dynamic conformational cycle of the group I chaperonin C-termini revealed via molecular dynamics simulation

• Percolation-like phase transitions in network models of protein dynamics

• Free energy landscape of activation in a signalling protein at atomic resolution

• A network of molecular switches controls the activation of the two-component response regulator NtrC

• Efficient maximum likelihood parameterization of continuous-time Markov processes

• Modeling molecular kinetics with tICA and the kernel trick

• Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics

• Conformational heterogeneity of the calmodulin binding interface

• Markov State Models and tICA Reveal a Nonnative Folding Nucleus in Simulations of NuG2

• Finding Our Way in the Dark Proteome

• Optimized parameter selection reveals trends in Markov state models for protein folding

• MSMBuilder: Statistical Models for Biomolecular Dynamics

• Identification of simple reaction coordinates from complex dynamics

• Ward Clustering Improves Cross-Validated Markov State Models of Protein Folding

• Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY

• Modeling the mechanism of CLN025 beta-hairpin formation

• A Minimum Variance Clustering Approach Produces Robust and Interpretable Coarse-Grained Models

• Markov State Models: From an Art to a Science

• Solving the RNA design problem with reinforcement learning

• Variational encoding of complex dynamics

• Overview of the SAMPL6 pKa challenge: evaluating small molecule microscopic and macroscopic pKa predictions

2020

• SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential

• Machine Learning Force Fields and Coarse-Grained Variables in Molecular Dynamics: Application to Materials and Biological Systems

• Citizen Scientists Create an Exascale Computer to Combat COVID-19

• Conformational distributions of isolated myosin motor domains encode their mechanochemical properties.

• Investigating Cryptic Binding Sites by Molecular Dynamics Simulations.

• Microcanonical coarse-graining of the kinetic Ising model.

• Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge.

• Standard state free energies, not pKas, are ideal for describing small molecule protonation and tautomeric states.

• The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.

• Spatial and temporal alterations in protein structure by EGF regulate cryptic cysteine oxidation.

• Adaptive Markov state model estimation using short reseeding trajectories.

• Reconciling simulated ensembles of apomyoglobin with experimental HDX data using Bayesian inference and multi-ensemble Markov State Models.

• The Cap-Snatching SFTSV Endonuclease Domain Is an Antiviral Target.

2019

• Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge.

• A Small-Molecule Pan-Id Antagonist Inhibits Pathologic Ocular Neovascularization.

• Ancestral reconstruction reveals mechanisms of ERK regulatory evolution.

• Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia.

• The dynamic conformational landscape of the protein methyltransferase SETD8.

• A Site-Specific ImmunoPET Tracer to Image PD-L1.

• Cooperative Changes in Solvent Exposure Identify Cryptic Pockets, Switches, and Allosteric Coupling.

• Fluorinated Aromatic Monomers as Building Blocks to Control α-Peptoid Conformation and Structure.

• What Makes a Kinase Promiscuous for Inhibitors?

2018

• Advanced Methods for Accessing Protein Shape-Shifting Present New Therapeutic Opportunities.

• Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY.

• Solving the RNA design problem with reinforcement learning.

• Overview of the SAMPL6 host-guest binding affinity prediction challenge.

• pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments.

• Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems.

• Escaping Atom Types in Force Fields Using Direct Chemical Perception.

• Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding.

• Simulations of the regulatory ACT domain of human phenylalanine hydroxylase unveil its mechanism of phenylalanine binding.

• Bayesian analysis of isothermal titration calorimetry for binding thermodynamics.

• An Open Library of Human Kinase Domain Constructs for Automated Bacterial Expression.

• Elucidating the inhibition of peptidoglycan biosynthesis in Staphylococcus aureus by albocycline, a macrolactone isolated from Streptomyces maizeus.

• Acquired resistance to IDH inhibition through trans or cis dimer-interface mutations.

• Variational encoding of complex dynamics.

• Biomolecular Simulations under Realistic Macroscopic Salt Conditions.

• Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo.

• Model Selection Using BICePs: A Bayesian Approach for Force Field Validation and Parameterization.

• Quantitative self-assembly prediction yields targeted nanomedicines.

• Transferable neural networks for enhanced sampling of protein dynamics.

• Electron Cryo-microscopy Structure of Ebola Virus Nucleoprotein Reveals a Mechanism for Nucleocapsid-like Assembly.

• A dynamic mechanism for allosteric activation of Aurora kinase A by activation loop phosphorylation.

• Theoretical restrictions on longest implicit time scales in Markov state models of biomolecular dynamics.

• REDOR NMR Reveals Multiple Conformers for a Protein Kinase C Ligand in a Membrane Environment.

• Warfarin traps human vitamin K epoxide reductase in an intermediate state during electron transfer.

• Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations.

• Markov State Models: From an Art to a Science.

• Mechanistic Basis for ATP-Dependent Inhibition of Glutamine Synthetase by Tabtoxinine-β-lactam.

2017

• Prediction of New Stabilizing Mutations Based on Mechanistic Insights from Markov State Models.

• A minimum variance clustering approach produces robust and interpretable coarse-grained models.

• Designing small molecules to target cryptic pockets yields both positive and negative allosteric modulators.

• Control of porphyrin interactions via structural changes of a peptoid scaffold.

• Bladder-cancer-associated mutations in RXRA activate peroxisome proliferator-activated receptors to drive urothelial proliferation.

• Millisecond dynamics of BTK reveal kinome-wide conformational plasticity within the apo kinase domain.

• Note: MSM lag time cannot be used for variational model selection.

• Molecular dynamics simulations reveal ligand-controlled positioning of a peripheral protein complex in membranes.

• Endogenous retinoid X receptor ligands in mouse hematopoietic cells.

• Solution-Phase Conformation and Dynamics of Conjugated Isoindigo-Based Donor-Acceptor Polymer Single Chains.

• Simulated Dynamics of Glycans on Ligand-Binding Domain of NMDA Receptors Reveals Strong Dynamic Coupling between Glycans and Protein Core.

• Transfer Learning from Markov Models Leads to Efficient Sampling of Related Systems.

• Modeling the mechanism of CLN025 beta-hairpin formation.

• Bridging Microscopic and Macroscopic Mechanisms of p53-MDM2 Binding with Kinetic Network Models.

• Identification of simple reaction coordinates from complex dynamics.

• Molecular simulations and free-energy calculations suggest conformation-dependent anion binding to a cytoplasmic site as a mechanism for Na+/K+-ATPase ion selectivity.

• Discovery of novel brain permeable and G protein-biased beta-1 adrenergic receptor partial agonists for the treatment of neurocognitive disorders.

• OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.

• Computational and Experimental Evaluation of Designed β-Cap Hairpins Using Molecular Simulations and Kinetic Network Models.

• Is Multitask Deep Learning Practical for Pharma?

• Precisely tuneable energy transfer system using peptoid helix-based molecular scaffold.

• MSMBuilder: Statistical Models for Biomolecular Dynamics.

• Diverted Total Synthesis of Carolacton-Inspired Analogs Yields Three Distinct Phenotypes in Streptococcus mutans Biofilms.

• L-2-Hydroxyglutarate production arises from noncanonical enzyme function at acidic pH.

• Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database.

• A water-mediated allosteric network governs activation of Aurora kinase A.

• Quantifying Allosteric Communication via Both Concerted Structural Changes and Conformational Disorder with CARDS.

• tICA-Metadynamics: Accelerating Metadynamics by using kinetically selected collective variables.

• Markov modeling reveals novel intracellular modulation of the human TREK-2 selectivity filter.

• Computationally Discovered Potentiating Role of Glycans on NMDA Receptors.

• Propagation of the Allosteric Modulation Induced by Sodium in the δ-Opioid Receptor.

2016

• A Maximum-Caliber Approach to Predicting Perturbed Folding Kinetics Due to Mutations.

• Defining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor.

• Training and Validation of a Liquid-Crystalline Phospholipid Bilayer Force Field.

• Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge.

• Structure and Dynamics of PD-L1 and an Ultra-High-Affinity PD-1 Receptor Mutant.

• Modelling proteins’ hidden conformations to predict antibiotic resistance.

• Mechanistically distinct cancer-associated mTOR activation clusters predict sensitivity to rapamycin

• Mechanistically distinct cancer-associated mTOR activation clusters predict sensitivity to rapamycin.

• Markov models of the apo-MDM2 lid region reveal diffuse yet two-state binding dynamics and receptor poses for computational docking.

• Transition path theory analysis of c-Src kinase activation.

• Finding Our Way in the Dark Proteome.

• Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale.

• Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale

• Markov State Models and tICA Reveal a Nonnative Folding Nucleus in Simulations of NuG2.

• Conformational heterogeneity of the calmodulin binding interface.

• Using Kinetic Network Models To Probe Non-Native Salt-Bridge Effects on α-Helix Folding.

2015

• Insights into Peptoid Helix Folding Cooperativity from an Improved Backbone Potential.

• FAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs.

• MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.

• Heat dissipation guides activation in signaling proteins.

• Efficient maximum likelihood parameterization of continuous-time Markov processes.

• United polarizable multipole water model for molecular mechanics simulation.

• OpenMM: A Hardware Independent Framework for Molecular Simulations.

• A network of molecular switches controls the activation of the two-component response regulator NtrC.

• Elucidating Ligand-Modulated Conformational Landscape of GPCRs Using Cloud-Computing Approaches.

• Variational cross-validation of slow dynamical modes in molecular kinetics.

• Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model.

• Markov state models provide insights into dynamic modulation of protein function.

• Cloud computing approaches for prediction of ligand binding poses and pathways.

• Corrigendum: Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways.

• Kinetic network models of tryptophan mutations in β-hairpins reveal the importance of non-native interactions.

2014

• Surprisal Metrics for Quantifying Perturbed Conformational Dynamics in Markov State Models.

• Activation pathway of Src kinase reveals intermediate states as targets for drug design.

• Statistical model selection for Markov models of biomolecular dynamics.

• Dynamical Phase Transitions Reveal Amyloid-like States on Protein Folding Landscapes.

• Describing protein folding via temperature-jump two-dimensional infrared spectroscopy and Markov state models.

• Cloud-based simulations on Google Exacycle reveal ligand-modulation of GPCR activation pathways.

2013

• Dynamics of an intrinsically disordered protein reveal metastable conformations that potentially seed aggregation

• Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics.

• Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9.

• Emergence of Glass-like Behavior in Markov State Models of Protein Folding Dynamics.

• To milliseconds and beyond: challenges in the simulation of protein folding.

• OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation.

• MSMExplorer: Visualizing Markov State Models for Biomolecule Folding Simulations.

• Building Markov state models with solvent dynamics

• Hierarchical Nyström methods for constructing Markov state models for conformational dynamics

2012

• Effects of familial mutations on the monomer structure of Aβ₄₂

• Mechanistic and structural insight into the functional dichotomy between IL-2 and IL-15.

• Marked difference in saxitoxin and tetrodotoxin affinity for the human nociceptive voltage-gated sodium channel (Nav1.7)

• Simple few-state models reveal hidden complexity in protein folding.

• Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment.

• Exploiting a natural conformational switch to engineer an interleukin-2 ‘superkine’

• Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer

• A Simple Model Predicts Experimental Folding Rates and a Hub-Like Topology

• Design of β-Amyloid Aggregation Inhibitors from a Predicted Structural Motif

• Mechanistic and structural insight into the functional dichotomy between IL-2 and IL-15

2011

• Rationally designed turn promoting mutation in the amyloid β-peptide sequence to stabilize oligomers in solution.

• Copernicus: A new paradigm for parallel adaptive molecular dynamics.

• Quantitative comparison of villin headpiece subdomain simulations and triplet–triplet energy transfer experiments.

• A smoothly decoupled particle interface (SDPI): new methods for coupling explicit and implicit solvent.

• Taming the complexity of protein folding.

• Atomistic folding simulations of the five helix bundle protein λ6-85.

2010

• Non-Bulk-Like Solvent Behavior in the Ribosome Exit Tunnel

• Speeding development and execution speed with Just In Time GPU code development approaches.

• Large-scale Chemical Informatics on the GPU.

• Hard Data on Soft Errors: A Large-Scale Assessment of Real-World Error Rates in GPGPU.

• Everything you wanted to know about Markov State Models but were afraid to ask.

• Protein folded states are kinetic hubs.

• Enhanced Modeling via Network Theory: Adaptive Sampling of Markov State Models.

• OpenMM: A Hardware Abstraction Layer for Molecular Simulations.

• Current Status of the AMOEBA Polarizable Force Field.

• Unfolded state dynamics and structure of protein L characterized by simulation and experiment.

• Network models for molecular kinetics and their initial applications to human health.

• Water Ordering at Membrane Interfaces Controls Fusion Dynamics

• Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics

• Evaluating Molecular Mechanical Potentials for Helical Peptides and Proteins.

• A simple theory of protein folding kinetics.

• Protein folded states are kinetic hubs.

• Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails.

• Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1−39)

2009

• Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint

• Combining Molecular Dynamics with Bayesian Analysis To Predict and Evaluate Ligand-Binding Mutations in Influenza Hemagglutinin.

• The Roles of Entropy and Kinetics in Structure Prediction.

• Using generalized ensemble simulations and Markov state models to identify conformational states.

• Folding@home: lessons from eight years of distributed computing.

• Probing the nanosecond dynamics of a designed three-stranded beta-sheet with massively parallel molecular dynamics simulation.

• A multiscale approach to sampling nascent peptide chains in the ribosomal exit tunnel.

• The Fip35 WW Domain Folds with Structural and Mechanistic Heterogeneity in Molecular Dynamics Simulations.

• Accelerating Molecular Dynamic Simulation on Graphics Processing Units.

• The predicted structure of the headpiece of the Huntingtin protein and its implications on Huntington aggregation

• Combining Mutual Information with Structural Analysis to Screen for Functionally Important Residues in Influenza Hemagglutinin.

• Accelerating Molecular Dynamic Simulation on the Cell processor and PlayStation 3

2008

• Side-chain recognition and gating in the ribosome exit tunnel

• Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach

• Structural Insight into RNA Hairpin Folding Intermediates

• Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment.

2007

• Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics

• Heterogeneity Even at the Speed Limit of Folding: Large-scale Molecular Dynamics Study of a Fast-folding Variant of the Villin Headpiece

• Control of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics.

• Persistent voids: a new structural metric for membrane fusion.

• Protein folding under confinement: a role for solvent.

• Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics.

• Storage@home: Petascale Distributed Storage

2006

• N-Body simulation on GPUs

• Predicting structure and dynamics of loosely-ordered protein complexes: influenza hemagglutinin fusion peptide.

• A Bayesian Update Method for Adaptive Weighted Sampling.

• Local structure formation in simulations of two small proteins.

• Kinetic Definition of Protein Folding Transition State Ensembles and Reaction Coordinates.

• Parallelized Over Parts Computation of Absolute Binding Free Energy with Docking and Molecular Dynamics.

• Folding Simulations of the Villin Headpiece in All-Atom Detail.

• Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion

• Electric Fields at the Active Site of an Enzyme: Direct Comparison of Experiment with Theory.

• Kinetic Computational Alanine Scanning: Application to p53 Oligomerization

• Validation of Markov state models using Shannon’s entropy.

• On the role of chemical detail in simulating protein folding kinetics.

• Nanotube confinement denatures protein helices.

• The solvation interface is a determining factor in peptide conformational preferences.

• Can conformational change be described by only a few normal modes?

2005

• How large is alpha-helix in solution? Studies of the radii of gyration of helical peptides by SAXS and MD.

• Error Analysis in Markovian State Models for protein folding.

• Direct calculation of the binding free energies of FKBP ligands using the Fujitsu BioServer massively parallel computer.

• A New Set of Molecular Mechanics Parameters for Hydroxyproline and Its Use in Molecular Dynamics Simulations of Collagen-Like Peptides.

• Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration.

• Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.

• Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water.

• Foldamer dynamics expressed via Markov state models. II. State space decomposition.

• Unusual compactness of a polyproline type II structure.

• How well can simulation predict protein folding kinetics and thermodynamics?

• Empirical Force-Field Assessment: The Interplay Between Backbone Torsions and Noncovalent Term Scaling.

• Exploring the Helix-Coil Transition via All-atom Equilibrium Ensemble Simulations.

• Does Water Play a Structural Role in the Folding of Small Nucleic Acids?

2004

• Dimerization of the p53 Oligomerization Domain: Identification of a Folding Nucleus by Molecular Dynamics Simulations.

• Using path sampling to build better Markovian state models: Predicting the folding rate and mechanism of a tryptophan zipper beta hairpin.

• Simulations of the role of water in the protein-folding mechanism.

• Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy.

• Does Native State Topology Determine the RNA Folding Mechanism?

2003

• Structural correspondence between the alpha-helix and the random-flight chain resolves how unfolded proteins can have native-like properties.

• Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood Methods.

• Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins.

• Solvent Viscosity Dependence of the Folding Rate of a Small Protein: Distributed Computing Study.

• https://foldingathome.org/papers/Sorin_etal_2003.pdf

• Multiplexed-Replica Exchange Molecular Dynamics Method for Protein Folding Simulation.

2002

• The Trp Cage: Folding Kinetics and Unfolded State Topology via Molecular Dynamics Simulations.

• Absolute comparison of simulated and experimental protein-folding dynamics.

• Native-like Mean Structure in the Unfolded Ensemble of Small Proteins.

• Simulation of Folding of a Small Alpha-helical Protein in Atomistic Detail using Worldwidedistributed Computing.

• Folding@home and Genome@Home: Using distributed computing to tackle previously intractable problems in computational biology.

• Atomistic protein folding simulations on the submillisecond timescale using worldwide distributed computing.

2001

• b-Hairpin Folding Simulations in Atomistic Detail Using an Implicit Solvent Model.

• Mathematical Foundations of ensemble dynamics.

2000

• Screen savers of the world, Unite!