HawkRank: a new scoring function for protein–protein docking based on weighted energy terms

Recent Advances in Protein-Protein Docking

(2016) Qian Zhang et al.   CURRENT DRUG TARGETS

Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein–protein binding free energies and re-rank binding poses generated by protein–protein docking

(2016) Fu Chen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

2P2Idb v2: update of a structural database dedicated to orthosteric modulation of protein–protein interactions

(2016) Marie-Jeanne Basse et al.   Database-The Journal of Biological Databases and Curation

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Flexibility and small pockets at protein–protein interfaces: New insights into druggability

(2015) Harry Jubb et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

PDB-wide collection of binding data: current status of the PDBbind database

(2014) Zhihai Liu et al.   BIOINFORMATICS

Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Origins of specificity and affinity in antibody–protein interactions

(2014) Hung-Pin Peng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution

(2013) Jessica Andreani et al.   BIOINFORMATICS

Inclusion of the orientational entropic effect and low-resolution experimental information for protein-protein docking in Critical Assessment of PRedicted Interactions (CAPRI)

(2013) Sheng-You Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

(2013) Rocco Moretti et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Drug-likeness analysis of traditional Chinese medicines: 2. Characterization of scaffold architectures for drug-like compounds, non-drug-like compounds, and natural compounds from traditional Chinese medicines

(2013) Sheng Tian et al.   Journal of Cheminformatics

2P2Idb: a structural database dedicated to orthosteric modulation of protein–protein interactions

(2012) Marie Jeanne Basse et al.   NUCLEIC ACIDS RESEARCH

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

COCOMAPS: a web application to analyze and visualize contacts at the interface of biomolecular complexes

(2011) A. Vangone et al.   BIOINFORMATICS

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

(2010) Tingjun Hou 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

Protein–protein docking tested in blind predictions: the CAPRI experiment

(2010) Joël Janin   Molecular BioSystems

Protein-protein docking with binding site patch prediction and network-based terms enhanced combinatorial scoring

(2010) Xinqi Gong et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-protein docking benchmark version 4.0

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

The road less traveled: modulating signal transduction enzymes by inhibiting their protein–protein interactions

(2009) Michelle R Arkin et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

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

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

Protein–protein interaction and quaternary structure

(2008) Joël Janin et al.   QUARTERLY REVIEWS OF BIOPHYSICS

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