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

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

SASpy: a PyMOL plugin for manipulation and refinement of hybrid models against small angle X-ray scattering data

(2016) Alejandro Panjkovich et al.   BIOINFORMATICS

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

(2016) Paweł Krupa et al.   BIOINFORMATICS

Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field

(2016) Magdalena A. Mozolewska et al.   Journal of Chemical Information and Modeling

Sampling Enrichment toward Target Structures Using Hybrid Molecular Dynamics-Monte Carlo Simulations

(2016) Kecheng Yang et al.   PLoS One

Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field

(2015) Paweł Krupa et al.   Journal of Chemical Information and Modeling

A Maximum-Likelihood Approach to Force-Field Calibration

(2015) Bartłomiej Zaborowski et al.   Journal of Chemical Information and Modeling

Deciphering Solution Scattering Data with Experimentally Guided Molecular Dynamics Simulations

(2015) Alexander Björling et al.   Journal of Chemical Theory and Computation

Physics-Based Potentials for the Coupling between Backbone- and Side-Chain-Local Conformational States in the United Residue (UNRES) Force Field for Protein Simulations

(2015) Adam K. Sieradzan et al.   Journal of Chemical Theory and Computation

SAXS-Guided Metadynamics

(2015) Dari Kimanius et al.   Journal of Chemical Theory and Computation

Template based protein structure modeling by global optimization in CASP11

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

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

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

Super-Resolution in Solution X-Ray Scattering and Its Applications to Structural Systems Biology

(2013) Robert P. Rambo et al.   Annual Review of Biophysics

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

Report of the wwPDB Small-Angle Scattering Task Force: Data Requirements for Biomolecular Modeling and the PDB

(2013) Jill Trewhella et al.   STRUCTURE

All-Atom Ensemble Modeling to Analyze Small-Angle X-Ray Scattering of Glycosylated Proteins

(2013) Miklos Guttman et al.   STRUCTURE

Combination of SAXS and NMR Techniques as a Tool for the Determination of Peptide Structure in Solution

(2010) Maciej Kozak et al.   Journal of Physical Chemistry Letters

Macromolecular docking restrained by a small angle X-ray scattering profile

(2010) Dina Schneidman-Duhovny et al.   JOURNAL OF STRUCTURAL BIOLOGY

FoXS: a web server for rapid computation and fitting of SAXS profiles

(2010) D. Schneidman-Duhovny et al.   NUCLEIC ACIDS RESEARCH

Homology modelling and spectroscopy, a never-ending love story

(2009) Hanka Venselaar et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Structure and flexibility within proteins as identified through small angle X-ray scattering

(2009) M. Pelikan et al.   GENERAL PHYSIOLOGY AND BIOPHYSICS

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

Exploring the parameter space of the coarse-grained UNRES force field by random search: Selecting a transferable medium-resolution force field

(2009) Yi He et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

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

Integration of Small-Angle X-Ray Scattering Data into Structural Modeling of Proteins and Their Assemblies

(2008) Friedrich Förster et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2008) Qiang Wang et al.   Nature Protocols

Normal-Mode Flexible Fitting of High-Resolution Structure of Biological Molecules toward One-Dimensional Low-Resolution Data

(2007) Christian Gorba et al.   BIOPHYSICAL JOURNAL