Modeling disordered protein interactions from biophysical principles

Coarse-Grained Protein Models and Their Applications

(2016) Sebastian Kmiecik et al.   CHEMICAL REVIEWS

FuzDB: database of fuzzy complexes, a tool to develop stochastic structure-function relationships for protein complexes and higher-order assemblies

(2016) Marton Miskei et al.   NUCLEIC ACIDS RESEARCH

DisProt 7.0: a major update of the database of disordered proteins

(2016) Damiano Piovesan et al.   NUCLEIC ACIDS RESEARCH

Human and server docking prediction for CAPRI round 30-35 using LZerD with combined scoring functions

(2016) Lenna X. Peterson et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure Prediction

(2016) Chengfei Yan et al.   STRUCTURE

Fuzzy complexes: Specific binding without complete folding

(2015) Rashmi Sharma et al.   FEBS LETTERS

GalaxyPepDock: a protein–peptide docking tool based on interaction similarity and energy optimization

(2015) Hasup Lee et al.   NUCLEIC ACIDS RESEARCH

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site

(2015) Mateusz Kurcinski et al.   NUCLEIC ACIDS RESEARCH

JPred4: a protein secondary structure prediction server

(2015) Alexey Drozdetskiy et al.   NUCLEIC ACIDS RESEARCH

ELM 2016—data update and new functionality of the eukaryotic linear motif resource

(2015) Holger Dinkel et al.   NUCLEIC ACIDS RESEARCH

Fully Blind Peptide-Protein Docking with pepATTRACT

(2015) Christina E.M. Schindler et al.   STRUCTURE

AnchorDock: Blind and Flexible Anchor-Driven Peptide Docking

(2015) Avraham Ben-Shimon et al.   STRUCTURE

SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity

(2014) C. N. Magnan et al.   BIOINFORMATICS

Protein-Protein Docking: From Interaction to Interactome

(2014) Ilya A. Vakser   BIOPHYSICAL JOURNAL

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Assessment of protein side-chain conformation prediction methods in different residue environments

(2014) Lenna X. Peterson et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Porter, PaleAle 4.0: high-accuracy prediction of protein secondary structure and relative solvent accessibility

(2013) C. Mirabello et al.   BIOINFORMATICS

Peptide docking and structure-based characterization of peptide binding: from knowledge to know-how

(2013) Nir London et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins

(2013) Mihaly Varadi et al.   NUCLEIC ACIDS RESEARCH

A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking

(2013) Mikael Trellet et al.   PLoS One

Detection of peptide-binding sites on protein surfaces: The first step toward the modeling and targeting of peptide-mediated interactions

(2013) Assaf Lavi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-Peptide Complex Prediction through Fragment Interaction Patterns

(2013) Erik Verschueren et al.   STRUCTURE

PepSite: prediction of peptide-binding sites from protein surfaces

(2012) L. G. Trabuco et al.   NUCLEIC ACIDS RESEARCH

Rate constants and mechanisms of intrinsically disordered proteins binding to structured targets

(2012) Huan-Xiang Zhou et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Fast and accurate prediction of protein side-chain conformations

(2011) Shide Liang et al.   BIOINFORMATICS

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

(2011) Hongyi Zhou et al.   BIOPHYSICAL JOURNAL

Molecular Surface Representation Using 3D Zernike Descriptors for Protein Shape Comparison and Docking

(2011) Daisuke Kihara et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors

(2011) Barak Raveh et al.   PLoS One

Generalized Fragment Picking in Rosetta: Design, Protocols and Applications

(2011) Dominik Gront et al.   PLoS One

Statistical mechanics-based method to extract atomic distance-dependent potentials from protein structures

(2011) Sheng-You Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A novel method for protein-protein interaction site prediction using phylogenetic substitution models

(2011) David La et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Automated Prediction of Protein Association Rate Constants

(2011) Sanbo Qin et al.   STRUCTURE

Structural and Dynamic Determinants of Protein-Peptide Recognition

(2011) Onur Dagliyan et al.   STRUCTURE

Intrinsic disorder: signaling via highly specific but short-lived association

(2011) Huan-Xiang Zhou   TRENDS IN BIOCHEMICAL SCIENCES

Computational Mapping of Anchoring Spots on Protein Surfaces

(2010) Avraham Ben-Shimon et al.   JOURNAL OF MOLECULAR BIOLOGY

Protein-protein docking using region-based 3D Zernike descriptors

(2009) Vishwesh Venkatraman et al.   BMC BIOINFORMATICS

DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility

(2009) Iris Antes   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners

(2008) Christopher J Oldfield et al.   BMC GENOMICS

Peptide-mediated interactions in biological systems: new discoveries and applications

(2008) Evangelia Petsalaki et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

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

Rapid comparison of properties on protein surface

(2008) Lee Sael et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

FACTS: Fast analytical continuum treatment of solvation

(2007) Urs Haberthür et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Efficient docking of peptides to proteins without prior knowledge of the binding site

(2002) Csaba Hetényi et al.   PROTEIN SCIENCE

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