The scoring of poses in protein-protein docking: current capabilities and future directions

SwarmDock: a server for flexible protein–protein docking

(2013) Mieczyslaw Torchala et al.   BIOINFORMATICS

Computational Peptidology: A New and Promising Approach to Therapeutic Peptide Design

(2013) P. Zhou et al.   CURRENT MEDICINAL CHEMISTRY

Biomacromolecular quantitative structure–activity relationship (BioQSAR): a proof-of-concept study on the modeling, prediction and interpretation of protein–protein binding affinity

(2013) Peng Zhou et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models

(2012) Iain H. Moal et al.   BIOINFORMATICS

Coarse-Grained Simulations of Protein-Protein Association: An Energy Landscape Perspective

(2012) Krishnakumar M. Ravikumar et al.   BIOPHYSICAL JOURNAL

Advances in the Prediction of Protein-Peptide Binding Affinities: Implications for Peptide-Based Drug Discovery

(2012) Joseph Audie et al.   Chemical Biology & Drug Design

Modulating Protein-Protein Interactions: From Structural Determinants of Binding to Druggability Prediction to Application

(2012) Alexander Metz et al.   CURRENT PHARMACEUTICAL DESIGN

Novel insights through the integration of structural and functional genomics data with protein networks

(2012) Declan Clarke et al.   JOURNAL OF STRUCTURAL BIOLOGY

Three-dimensional reconstruction of protein networks provides insight into human genetic disease

(2012) Xiujuan Wang et al.   NATURE BIOTECHNOLOGY

Predictive energy landscapes for protein-protein association

(2012) W. Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prediction of protein-protein binding free energies

(2012) Thom Vreven et al.   PROTEIN SCIENCE

Designing specific protein-protein interactions using computation, experimental library screening, or integrated methods

(2012) T. Scott Chen et al.   PROTEIN SCIENCE

Scoring protein interaction decoys using exposed residues (SPIDER): A novel multibody interaction scoring function based on frequent geometric patterns of interfacial residues

(2012) Raed Khashan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structural Data in Synthetic Biology Approaches for Studying General Design Principles of Cellular Signaling Networks

(2012) Christina Kiel et al.   STRUCTURE

Kinetic Rate Constant Prediction Supports the Conformational Selection Mechanism of Protein Binding

(2012) Iain H. Moal et al.   PLoS Computational Biology

Structure-based prediction of protein–protein binding affinity with consideration of allosteric effect

(2011) Feifei Tian et al.   AMINO ACIDS

Protein–protein binding affinity prediction on a diverse set of structures

(2011) Iain H. Moal et al.   BIOINFORMATICS

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

(2011) Hongyi Zhou et al.   BIOPHYSICAL JOURNAL

DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking

(2011) Shiyong Liu et al.   BMC BIOINFORMATICS

Prediction of protein-binding areas by small-world residue networks and application to docking

(2011) Carles Pons et al.   BMC BIOINFORMATICS

Three-dimensional modeling of protein interactions and complexes is going ‘omics

(2011) Amelie Stein et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Druggability assessment of protein–protein interfaces

(2011) Jutta Wanner et al.   Future Medicinal Chemistry

Structure-based computational analysis of protein binding sites for function and druggability prediction

(2011) Britta Nisius et al.   JOURNAL OF BIOTECHNOLOGY

Scoring by Intermolecular Pairwise Propensities of Exposed Residues (SIPPER): A New Efficient Potential for Protein−Protein Docking

(2011) Carles Pons et al.   Journal of Chemical Information and Modeling

PROCOS: Computational analysis of protein-protein complexes

(2011) Florian Fink et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology

(2011) Sarel J. Fleishman et al.   JOURNAL OF MOLECULAR BIOLOGY

A Collaborative Filtering Approach for Protein-Protein Docking Scoring Functions

(2011) Thomas Bourquard et al.   PLoS One

On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking

(2011) Elisenda Feliu et al.   PROTEIN SCIENCE

Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions

(2011) Nitin Bhardwaj et al.   PROTEIN SCIENCE

A structure-based benchmark for protein-protein binding affinity

(2011) Panagiotis L. Kastritis et al.   PROTEIN SCIENCE

Effects of point mutations in pVHL on the binding of HIF-1α

(2011) Carmen Domene et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Surface-histogram: A new shape descriptor for protein-protein docking

(2011) Shengyin Gu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Novel high-affinity binders of human interferon gamma derived from albumin-binding domain of protein G

(2011) Jawid N. Ahmad et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A Multidomain Flexible Docking Approach to Deal with Large Conformational Changes in the Modeling of Biomolecular Complexes

(2011) Ezgi Karaca et al.   STRUCTURE

Diffusion and association processes in biological systems: theory, computation and experiment

(2011) Paolo Mereghetti et al.   BMC Biophysics

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

(2010) S. Chaudhury et al.   BIOINFORMATICS

Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials

(2010) Yaping Feng et al.   BMC BIOINFORMATICS

New measures for estimating surface complementarity and packing at protein-protein interfaces

(2010) Pralay Mitra et al.   FEBS LETTERS

SwarmDock and the Use of Normal Modes in Protein-Protein Docking

(2010) Iain H. Moal et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Using correlated parameters for improved ranking of protein-protein docking decoys

(2010) Pralay Mitra et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Are Scoring Functions in Protein−Protein Docking Ready To Predict Interactomes? Clues from a Novel Binding Affinity Benchmark

(2010) Panagiotis L. Kastritis et al.   JOURNAL OF PROTEOME RESEARCH

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

Detection and refinement of encounter complexes for protein-protein docking: Taking account of macromolecular crowding

(2010) Xiaofan Li et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Accounting for conformational entropy in predicting binding free energies of protein-protein interactions

(2010) Hetunandan Kamisetty et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Predicting protein flexibility through the prediction of local structures

(2010) Aurélie Bornot et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-protein docking benchmark version 4.0

(2010) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Designing coarse grained-and atom based-potentials for protein-protein docking

(2010) Dror Tobi   BMC STRUCTURAL BIOLOGY

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

(2009) Vishwesh Venkatraman et al.   BMC BIOINFORMATICS

Fundamental Aspects of Protein−Protein Association Kinetics

(2009) G. Schreiber et al.   CHEMICAL REVIEWS

Predicting protein protein interfaces as clusters of Optimal Docking Area points

(2009) Yasir Arafat et al.   International Journal of Data Mining and Bioinformatics

Towards inferring time dimensionality in protein–protein interaction networks by integrating structures: the p53 example

(2009) Nurcan Tuncbag et al.   Molecular BioSystems

Fast predictions of thermodynamics and kinetics of protein–protein recognition from structures: from molecular design to systems biology

(2009) Daniele Dell’Orco   Molecular BioSystems

Computer-aided design of functional protein interactions

(2009) Daniel J Mandell et al.   Nature Chemical Biology

Predicting protein complex geometries with a neural network

(2009) Myong-Ho Chae et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

PTools: an opensource molecular docking library

(2009) Adrien Saladin et al.   BMC STRUCTURAL BIOLOGY

Analyzing Protein Interaction Networks Using Structural Information

(2008) Christina Kiel et al.   Annual Review of Biochemistry

FunHunt: model selection based on energy landscape characteristics

(2008) Nir London et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Amino acid network and its scoring application in protein–protein docking

(2008) Shan Chang et al.   BIOPHYSICAL CHEMISTRY

DARS (Decoys As the Reference State) Potentials for Protein-Protein Docking

(2008) Gwo-Yu Chuang et al.   BIOPHYSICAL JOURNAL

2D depiction of nonbonding interactions for protein complexes

(2008) Peng Zhou et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Predicting free energy changes using structural ensembles

(2008) Alexander Benedix et al.   NATURE METHODS

Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking

(2008) S. E. Dobbins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions

(2008) Yuedong Yang et al.   PROTEIN SCIENCE

Discrimination of near-native structures in protein-protein docking by testing the stability of local minima

(2008) Dima Kozakov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A combination of rescoring and refinement significantly improves protein docking performance

(2008) Brian Pierce et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

An iterative knowledge-based scoring function for protein-protein recognition

(2008) Sheng-You Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

Funnel Hunting in a Rough Terrain: Learning and Discriminating Native Energy Funnels

(2008) Nir London et al.   STRUCTURE

OPUS-PSP: An Orientation-dependent Statistical All-atom Potential Derived from Side-chain Packing

(2007) Mingyang Lu et al.   JOURNAL OF MOLECULAR BIOLOGY