Computational protein structure refinement: almost there, yet still so far to go

Performance of protein-structure predictions with the physics-based UNRES force field in CASP11

(2016) Paweł Krupa et al.   BIOINFORMATICS

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

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

Local Protein Structure Refinement via Molecular Dynamics Simulations with locPREFMD

(2016) Michael Feig   Journal of Chemical Information and Modeling

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

(2016) Jing Huang et al.   NATURE METHODS

3Drefine: an interactive web server for efficient protein structure refinement

(2016) Debswapna Bhattacharya et al.   NUCLEIC ACIDS RESEARCH

Critical assessment of methods of protein structure prediction: Progress and new directions in round XI

(2016) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of refinement of template-based models in CASP11

(2016) Vivek Modi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm

(2016) Isseki Yu et al.   eLife

Blind protein structure prediction using accelerated free-energy simulations

(2016) A. Perez et al.   Science Advances

Benchmarking Deep Networks for Predicting Residue-Specific Quality of Individual Protein Models in CASP11

(2016) Tong Liu et al.   Scientific Reports

An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution

(2015) Aaron M. Fluitt et al.   BIOPHYSICAL JOURNAL

Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics—Monte Carlo Simulations Guided by a Coarse-Grained Model

(2015) Yunjie Chen et al.   Journal of Chemical Theory and Computation

Coupling an Ensemble of Homologues Improves Refinement of Protein Homology Models

(2015) André Wildberg et al.   Journal of Chemical Theory and Computation

Significant Refinement of Protein Structure Models Using a Residue-Specific Force Field

(2015) Sangni Xun et al.   Journal of Chemical Theory and Computation

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States

(2015) Stefano Piana et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein structure prediction provides comparable performance to crystallographic structures in docking-based virtual screening

(2015) Hongying Du et al.   METHODS

Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics

(2015) Avishek Kumar et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Template-based protein structure prediction in CASP11 and retrospect of I-TASSER in the last decade

(2015) Jianyi Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein structure refinement with adaptively restrained homologous replicas

(2015) Dennis Della Corte et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

CASP11 refinement experiments with ROSETTA

(2015) Hahnbeom Park et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Selective refinement and selection of near-native models in protein structure prediction

(2015) Jiong Zhang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein structure refinement by optimization

(2015) Martin Carlsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein structure refinement via molecular-dynamics simulations: What works and what does not?

(2015) Michael Feig et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Effective protein model structure refinement by loop modeling and overall relaxation

(2015) Gyu Rie Lee et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Origin of Consistent Protein Structure Refinement from Structural Averaging

(2015) Hahnbeom Park et al.   STRUCTURE

Protein Structure Refinement of CASP Target Proteins Using GNEIMO Torsional Dynamics Method

(2014) Adrien B. Larsen et al.   Journal of Chemical Information and Modeling

Accelerate Sampling in Atomistic Energy Landscapes Using Topology-Based Coarse-Grained Models

(2014) Weihong Zhang et al.   Journal of Chemical Theory and Computation

Balanced Protein–Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association

(2014) Robert B. Best et al.   Journal of Chemical Theory and Computation

Residue-Specific Force Field Based on Protein Coil Library. RSFF2: Modification of AMBER ff99SB

(2014) Chen-Yang Zhou et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Evaluation of Unrestrained Replica-Exchange Simulations Using Dynamic Walkers in Temperature Space for Protein Structure Refinement

(2014) Mark A. Olson et al.   PLoS One

Computational modeling of membrane proteins

(2014) Julia Koehler Leman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

(2013) Cameron Abrams et al.   Entropy

PRIMO: A Transferable Coarse-Grained Force Field for Proteins

(2013) Parimal Kar et al.   Journal of Chemical Theory and Computation

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

Reaching new levels of realism in modeling biological macromolecules in cellular environments

(2013) Michael Feig et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

GalaxyRefine: protein structure refinement driven by side-chain repacking

(2013) Lim Heo et al.   NUCLEIC ACIDS RESEARCH

i3Drefine Software for Protein 3D Structure Refinement and Its Assessment in CASP10

(2013) Debswapna Bhattacharya et al.   PLoS One

Structure refinement of protein model decoys requires accurate side-chain placement

(2013) Mark A. Olson et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

3Drefine: Consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization

(2013) Debswapna Bhattacharya et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

CASP10 results compared to those of previous CASP experiments

(2013) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Princeton_TIGRESS: Protein geometry refinement using simulations and support vector machines

(2013) George A. Khoury et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging

(2013) Vahid Mirjalili et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of template-based protein structure predictions in CASP10

(2013) Yuanpeng J. Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Evaluation of predictions in the CASP10 model refinement category

(2013) Timothy Nugent et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

BCL::MP-Fold: Folding Membrane Proteins through Assembly of Transmembrane Helices

(2013) Brian E. Weiner et al.   STRUCTURE

Inclusion of Many-Body Effects in the Additive CHARMM Protein CMAP Potential Results in Enhanced Cooperativity of α-Helix and β-Hairpin Formation

(2012) Robert B. Best et al.   BIOPHYSICAL JOURNAL

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

(2012) Thomas J Lane et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations

(2012) Elio A. Cino et al.   Journal of Chemical Theory and Computation

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles

(2012) Vahid Mirjalili et al.   Journal of Chemical Theory and Computation

Membrane protein native state discrimination by implicit membrane models

(2012) Olga Yuzlenko et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structure Refinement of Protein Low Resolution Models Using the GNEIMO Constrained Dynamics Method

(2012) In-Hee Park et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structure and Dynamics of an Unfolded Protein Examined by Molecular Dynamics Simulation

(2012) Kresten Lindorff-Larsen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

KoBaMIN: a knowledge-based minimization web server for protein structure refinement

(2012) J. P. G. L. M. Rodrigues et al.   NUCLEIC ACIDS RESEARCH

GalaxyWEB server for protein structure prediction and refinement

(2012) J. Ko et al.   NUCLEIC ACIDS RESEARCH

Systematic Validation of Protein Force Fields against Experimental Data

(2012) Kresten Lindorff-Larsen et al.   PLoS One

Optimization of protein models

(2012) Dominik Gront et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Modelling dynamics in protein crystal structures by ensemble refinement

(2012) B Tom Burnley et al.   eLife

Chemical Cross-Linking and H/D Exchange for Fast Refinement of Protein Crystal Structure

(2011) Daniel Rozbesky et al.   ANALYTICAL CHEMISTRY

GOAP: A Generalized Orientation-Dependent, All-Atom Statistical Potential for Protein Structure Prediction

(2011) Hongyi Zhou et al.   BIOPHYSICAL JOURNAL

Homology Models in Docking and High-Throughput Docking

(2011) Claudio N. Cavasotto   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Comparison between self-guided Langevin dynamics and molecular dynamics simulations for structure refinement of protein loop conformations

(2011) Mark A. Olson et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Exploring the Folding Free Energy Landscape of a β-Hairpin Miniprotein, Chignolin, Using Multiscale Free Energy Landscape Calculation Method

(2011) Ryuhei Harada et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Refinement of protein termini in template-based modeling using conformational space annealing

(2011) Hahnbeom Park et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of protein structure refinement in CASP9

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

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Atomic-Level Protein Structure Refinement Using Fragment-Guided Molecular Dynamics Conformation Sampling

(2011) Jian Zhang et al.   STRUCTURE

SAXS Ensemble Refinement of ESCRT-III CHMP3 Conformational Transitions

(2011) Bartosz Różycki et al.   STRUCTURE

New statistical potential for quality assessment of protein models and a survey of energy functions

(2010) Dmitry Rykunov et al.   BMC BIOINFORMATICS

Beyond directed evolution—semi-rational protein engineering and design

(2010) Stefan Lutz   CURRENT OPINION IN BIOTECHNOLOGY

Protein Folding Simulations Combining Self-Guided Langevin Dynamics and Temperature-Based Replica Exchange

(2010) Michael S. Lee et al.   Journal of Chemical Theory and Computation

Predicting the accuracy of protein-ligand docking on homology models

(2010) Annalisa Bordogna et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Reliable protein structure refinement using a physical energy function

(2010) Matthew S. Lin et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Simulations of a Protein Crystal with a High Resolution X-ray Structure: Evaluation of Force Fields and Water Models

(2010) David S. Cerutti et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure Prediction

(2010) Jian Zhang et al.   PLoS One

Principles of protein folding - A perspective from simple exact models

(2010) Ken A. Dill et al.   PROTEIN SCIENCE

Dynameomics: A Comprehensive Database of Protein Dynamics

(2010) Marc W. van der Kamp et al.   STRUCTURE

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Convergence and combination of methods in protein–protein docking

(2009) Sandor Vajda et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Protein structure prediction: when is it useful?

(2009) Yang Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY

Hydrogen Bonding and π-Stacking: How Reliable are Force Fields? A Critical Evaluation of Force Field Descriptions of Nonbonded Interactions

(2009) Robert S. Paton et al.   Journal of Chemical Information and Modeling

Prediction of membrane protein structures with complex topologies using limited constraints

(2009) P. Barth et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessment of the protein-structure refinement category in CASP8

(2009) Justin L. MacCallum et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy

(2009) Srinivasa M. Gopal et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Development of a Physics-Based Force Field for the Scoring and Refinement of Protein Models

(2008) Liliana Wroblewska et al.   BIOPHYSICAL JOURNAL

Recent advances in implicit solvent-based methods for biomolecular simulations

(2008) Jianhan Chen et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data

(2008) Alexander Grishaev et al.   JOURNAL OF BIOMOLECULAR NMR

Prediction of Protein Loop Conformations Using the AGBNP Implicit Solvent Model and Torsion Angle Sampling

(2008) Anthony K. Felts et al.   Journal of Chemical Theory and Computation

ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutions

(2008) Andreas Vitalis et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Refinement of comparative models of protein structure by using multicanonical molecular dynamics simulations

(2008) Ryuichiro Ishitani et al.   MOLECULAR SIMULATION

Protein model refinement using an optimized physics-based all-atom force field

(2008) A. Jagielska et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Solvent dramatically affects protein structure refinement

(2008) G. Chopra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Specific interactions for ab initio folding of protein terminal regions with secondary structures

(2008) Yuedong Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Refining homology models by combining replica-exchange molecular dynamics and statistical potentials

(2008) Jiang Zhu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A multi-template combination algorithm for protein comparative modeling

(2008) Jianlin Cheng   BMC STRUCTURAL BIOLOGY

Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions

(2007) Mark A. Olson et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

(2002) Hongyi Zhou et al.   PROTEIN SCIENCE