Protein storytelling through physics

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

Principles for Integrative Structural Biology Studies

(2019) Michael P. Rout et al.   CELL

Advances in enhanced sampling molecular dynamics simulations for biomolecules

(2019) An-hui Wang et al.   CHINESE JOURNAL OF CHEMICAL PHYSICS

Reports from the fifth edition of CAGI: The Critical Assessment of Genome Interpretation

(2019) Gaia Andreoletti et al.   HUMAN MUTATION

Evaluation of model refinement in CASP13

(2019) Randy J. Read et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structural modeling of protein complexes: Current capabilities and challenges

(2019) Justas Dapkūnas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

NMR‐assisted protein structure prediction with MELDxMD

(2019) James C. Robertson et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improving the Efficiency of Ligand-Binding Protein Design with Molecular Dynamics Simulations

(2019) Emilia P. Barros et al.   Journal of Chemical Theory and Computation

Blinded prediction of protein–ligand binding affinity using Amber thermodynamic integration for the 2018 D3R grand challenge 4

(2019) Junjie Zou et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Anthropogenic biases in chemical reaction data hinder exploratory inorganic synthesis

(2019) Xiwen Jia et al.   NATURE

Distance-based protein folding powered by deep learning

(2019) Jinbo Xu   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Encounter complexes and hidden poses of kinase-inhibitor binding on the free-energy landscape

(2019) Suyong Re et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluation of template‐based modeling in CASP13

(2019) Tristan I. Croll et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Machine learning transforms how microstates are sampled

(2019) Mark E. Tuckerman   SCIENCE

Boltzmann generators: Sampling equilibrium states of many-body systems with deep learning

(2019) Frank Noé et al.   SCIENCE

Dissecting the Energetics of Intrinsically Disordered Proteins via a Hybrid Experimental and Computational Approach

(2019) Junjie Zou et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein structure prediction assisted with sparse NMR data in CASP13

(2019) Davide Sala et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment

(2019) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution

(2019) Chuan Tian et al.   Journal of Chemical Theory and Computation

Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4

(2019) Sergei Kotelnikov et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Modeling beta‐sheet peptide‐protein interactions: Rosetta FlexPepDock in CAPRI rounds 38‐45

(2019) Alisa Khramushin et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Unbiased Molecular Dynamics of 11 min Timescale Drug Unbinding Reveals Transition State Stabilizing Interactions

(2018) Samuel D Lotz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Developing a molecular dynamics force field for both folded and disordered protein states

(2018) Paul Robustelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Escaping Atom Types in Force Fields Using Direct Chemical Perception

(2018) David L. Mobley et al.   Journal of Chemical Theory and Computation

MELD × MD Folds Nonthreadables, Giving Native Structures and Populations

(2018) James C. Robertson et al.   Journal of Chemical Theory and Computation

Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database

(2017) Guilherme Duarte Ramos Matos et al.   JOURNAL OF CHEMICAL AND ENGINEERING DATA

Molecular Simulations Identify Binding Poses and Approximate Affinities of Stapled α-Helical Peptides to MDM2 and MDMX

(2017) Joseph A. Morrone et al.   Journal of Chemical Theory and Computation

Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15

(2017) Lee-Ping Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations

(2017) Matteo Aldeghi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The ClusPro web server for protein–protein docking

(2017) Dima Kozakov et al.   Nature Protocols

How and when does an anticancer drug leave its binding site?

(2017) Pratyush Tiwary et al.   Science Advances

Coarse-Grained Protein Models and Their Applications

(2016) Sebastian Kmiecik et al.   CHEMICAL REVIEWS

Advances in free-energy-based simulations of protein folding and ligand binding

(2016) Alberto Perez et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model

(2016) Karl T. Debiec et al.   Journal of Chemical Theory and Computation

D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions

(2016) Symon Gathiaka et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

(2016) G.C.P. van Zundert et al.   JOURNAL OF MOLECULAR BIOLOGY

Markovian and Non-Markovian Modeling of Membrane Dynamics with Milestoning

(2016) Alfredo E. Cardenas et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Experimental and Computational Analysis of Protein Stabilization by Gly-to-d-Ala Substitution: A Convolution of Native State and Unfolded State Effects

(2016) Junjie Zou et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

(2016) Jing Huang et al.   NATURE METHODS

Blind protein structure prediction using accelerated free-energy simulations

(2016) A. Perez et al.   Science Advances

Enhanced sampling techniques in molecular dynamics simulations of biological systems

(2015) Rafael C. Bernardi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Amyloid β Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies

(2015) Jessica Nasica-Labouze et al.   CHEMICAL REVIEWS

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

(2015) Edward Harder et al.   Journal of Chemical Theory and Computation

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

(2015) Lingle Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The drug–target residence time model: a 10-year retrospective

(2015) Robert A. Copeland   NATURE REVIEWS DRUG DISCOVERY

Accelerating molecular simulations of proteins using Bayesian inference on weak information

(2015) Alberto Perez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference

(2015) Justin L. MacCallum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning

(2015) Lane W. Votapka et al.   PLoS Computational Biology

A Structural and Energetic Model for the Slow-Onset Inhibition of the Mycobacterium tuberculosis Enoyl-ACP Reductase InhA

(2014) Huei-Jiun Li et al.   ACS Chemical Biology

Blind prediction of HIV integrase binding from the SAMPL4 challenge

(2014) David L. Mobley et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge

(2014) Emilio Gallicchio et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Folding Simulations for Proteins with Diverse Topologies Are Accessible in Days with a Physics-Based Force Field and Implicit Solvent

(2014) Hai Nguyen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator

(2013) Pedro E. M. Lopes et al.   Journal of Chemical Theory and Computation

A large-scale evaluation of computational protein function prediction

(2013) Predrag Radivojac et al.   NATURE METHODS

Mechanism of IAPP amyloid fibril formation involves an intermediate with a transient  -sheet

(2013) L. E. Buchanan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Kinetic characterization of the critical step in HIV-1 protease maturation

(2012) S. K. Sadiq et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding

(2012) A. T. Fenley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field

(2012) Dong Xu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies

(2012) Daniel Russel et al.   PLOS BIOLOGY

Role of Water in Protein Aggregation and Amyloid Polymorphism

(2011) D. Thirumalai et al.   ACCOUNTS OF CHEMICAL RESEARCH

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

How Does a Drug Molecule Find Its Target Binding Site?

(2011) Yibing Shan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations

(2011) I. Buch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessment of protein structure refinement in CASP9

(2011) Justin L. MacCallum et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Free Energy Landscape of Small Molecule Unbinding

(2011) Danzhi Huang et al.   PLoS Computational Biology

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site

(2009) Sarah E. Boyce et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2009) Gregory R. Bowman et al.   METHODS

Anton, a special-purpose machine for molecular dynamics simulation

(2008) David E. Shaw et al.   COMMUNICATIONS OF THE ACM

Coarse Master Equations for Peptide Folding Dynamics†

(2008) Nicolae-Viorel Buchete et al.   JOURNAL OF PHYSICAL CHEMISTRY B