Introduction of a bounded penalty function in contact‐assisted simulations of protein structures to omit false restraints

DeepCDpred: Inter-residue distance and contact prediction for improved prediction of protein structure

(2019) Shuangxi Ji et al.   PLoS One

Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: Test with CASP12 targets

(2018) Agnieszka Karczyńska et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

(2018) Chen Keasar et al.   Scientific Reports

Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study

(2018) Björn Hellenkamp et al.   NATURE METHODS

Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics

(2017) Paweł Krupa et al.   Journal of Chemical Information and Modeling

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. I. Backbone potentials of coarse-grained polypeptide chains

(2017) Adam K. Sieradzan et al.   JOURNAL OF CHEMICAL PHYSICS

Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins

(2017) Agnieszka S. Karczyńska et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Introduction of steered molecular dynamics into UNRES coarse-grained simulations package

(2017) Adam K. Sieradzan et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information

(2017) Agnieszka S. Karczyńska et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Critical assessment of methods of protein structure prediction (CASP)-Round XII

(2017) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Applications of contact predictions to structural biology

(2017) Felix Simkovic et al.   IUCrJ

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

(2016) Paweł Krupa et al.   BIOINFORMATICS

Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems

(2016) Mykola Dimura et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

conSSert: Consensus SVM Model for Accurate Prediction of Ordered Secondary Structure

(2016) Chris A. Kieslich et al.   Journal of Chemical Information and Modeling

CoinFold: a web server for protein contact prediction and contact-assisted protein folding

(2016) Sheng Wang et al.   NUCLEIC ACIDS RESEARCH

Contact-assisted protein structure modeling by global optimization in CASP11

(2016) Keehyoung Joo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of CASP11 contact-assisted predictions

(2016) Lisa N. Kinch et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein structure determination by combining sparse NMR data with evolutionary couplings

(2015) Yuefeng Tang et al.   NATURE METHODS

xVis: a web server for the schematic visualization and interpretation of crosslink-derived spatial restraints

(2015) Maximilian Grimm et al.   NUCLEIC ACIDS RESEARCH

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

Protein structure determination by conformational space annealing using NMR geometric restraints

(2015) Keehyoung Joo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11

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

CCMpred—fast and precise prediction of protein residue–residue contacts from correlated mutations

(2014) Stefan Seemayer et al.   BIOINFORMATICS

Revised Backbone-Virtual-Bond-Angle Potentials to Treat the l- and d-Amino Acid Residues in the Coarse-Grained United Residue (UNRES) Force Field

(2014) Adam K. Sieradzan et al.   Journal of Chemical Theory and Computation

A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions

(2014) Adam Liwo et al.   JOURNAL OF MOLECULAR MODELING

Chemical cross-linking/mass spectrometry targeting acidic residues in proteins and protein complexes

(2014) Alexander Leitner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

WeFold: A coopetition for protein structure prediction

(2014) George A. Khoury et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improvement of the Treatment of Loop Structures in the UNRES Force Field by Inclusion of Coupling between Backbone- and Side-Chain-Local Conformational States

(2013) Paweł Krupa et al.   Journal of Chemical Theory and Computation

Scalable web services for the PSIPRED Protein Analysis Workbench

(2013) Daniel W. A. Buchan et al.   NUCLEIC ACIDS RESEARCH

Lessons from application of the UNRES force field to predictions of structures of CASP10 targets

(2013) Y. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013) H. Kamisetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein structure modeling for CASP10 by multiple layers of global optimization

(2013) Keehyoung Joo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Critical assessment of methods of protein structure prediction (CASP) - round x

(2013) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

CABS-NMR-De novo tool for rapid global fold determination from chemical shifts, residual dipolar couplings and sparse methyl-methyl noes

(2010) Dorota Latek et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins

(2009) Cezary Czaplewski et al.   Journal of Chemical Theory and Computation

Protein contact order prediction from primary sequences

(2008) Yi Shi et al.   BMC BIOINFORMATICS

Fast procedure for reconstruction of full-atom protein models from reduced representations

(2008) Piotr Rotkiewicz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Optimized Explicit-Solvent Replica Exchange Molecular Dynamics from Scratch

(2008) Walter Nadler et al.   JOURNAL OF PHYSICAL CHEMISTRY B

SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling

(2008) Qiang Wang et al.   Nature Protocols

Improving NMR protein structure quality by Rosetta refinement: A molecular replacement study

(2008) Theresa A. Ramelot et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS