Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13

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

(2019) Emilia A. Lubecka et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CASP13 target classification into tertiary structure prediction categories

(2019) Lisa N. Kinch et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Small angle X-ray scattering and cross-linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy

(2018) Tadeusz L. Ogorzalek et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Modeling Protein Complexes Using Restraints from Crosslinking Mass Spectrometry

(2018) Joshua Matthew Allen Bullock et al.   STRUCTURE

Comparative analysis of methods for evaluation of protein models against native structures

(2018) Kliment Olechnovič et al.   BIOINFORMATICS

Smooth orientation-dependent scoring function for coarse-grained protein quality assessment

(2018) Mikhail Karasikov et al.   BIOINFORMATICS

In-Search Assignment of Monoisotopic Peaks Improves the Identification of Cross-Linked Peptides

(2018) Swantje Lenz et al.   JOURNAL OF PROTEOME RESEARCH

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

NOLB: Nonlinear Rigid Block Normal-Mode Analysis Method

(2017) Alexandre Hoffmann et al.   Journal of Chemical Theory and Computation

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

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

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

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

The Importance of Non-accessible Crosslinks and Solvent Accessible Surface Distance in Modeling Proteins with Restraints From Crosslinking Mass Spectrometry

(2016) Joshua Matthew Allen Bullock et al.   MOLECULAR & CELLULAR PROTEOMICS

2016 update of the PRIDE database and its related tools

(2016) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Blind testing of cross-linking/mass spectrometry hybrid methods in CASP11

(2016) Michael Schneider et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Blind Evaluation of Hybrid Protein Structure Analysis Methods based on Cross-Linking

(2016) Adam Belsom et al.   TRENDS IN BIOCHEMICAL SCIENCES

A Study into the Collision-induced Dissociation (CID) Behavior of Cross-Linked Peptides

(2015) Sven H. Giese et al.   MOLECULAR & CELLULAR PROTEOMICS

Serum Albumin Domain Structures in Human Blood Serum by Mass Spectrometry and Computational Biology

(2015) Adam Belsom et al.   MOLECULAR & CELLULAR PROTEOMICS

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

lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests

(2013) Valerio Mariani et al.   BIOINFORMATICS

Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline

(2013) Alexander Leitner et al.   Nature Protocols

False discovery rate estimation for cross-linked peptides identified by mass spectrometry

(2012) Thomas Walzthoeni et al.   NATURE METHODS

Photo-assisted peptide enrichment in protein complex cross-linking analysis of a model homodimeric protein using mass spectrometry

(2011) Funing Yan et al.   PROTEOMICS

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

(2010) Dmitry Rykunov et al.   BMC BIOINFORMATICS

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