Papers & Results

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

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

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

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

• 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

• 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.

• 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?

• 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.

• 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.

• 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.

• 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.

• 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.

• 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

• 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

• 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.

• 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)

• 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

• 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.

• 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

• 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?

• 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?

• 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?

• 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.

• 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.

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

• Mathematical Foundations of ensemble dynamics.

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