Development of a new benchmark for assessing the scoring functions applicable to protein–protein interactions

Performance of machine-learning scoring functions in structure-based virtual screening

(2017) Maciej Wójcikowski et al.   Scientific Reports

Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition

(2016) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Selective Targeting of the TPX2 Site of Importin-α Using Fragment-Based Ligand Design

(2015) Rhian S. Holvey et al.   ChemMedChem

High-resolution protein–protein docking by global optimization: recent advances and future challenges

(2015) Hahnbeom Park et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Exploring the potential of global protein–protein docking: an overview and critical assessment of current programs for automatic ab initio docking

(2015) Sheng-You Huang   DRUG DISCOVERY TODAY

Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2

(2015) Thom Vreven et al.   JOURNAL OF MOLECULAR BIOLOGY

High-resolution crystal structures leverage protein binding affinity predictions

(2015) Simon Marillet et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening

(2015) Qurrat Ul Ain et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

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

(2014) Zhihai Liu et al.   BIOINFORMATICS

Search strategies and evaluation in protein–protein docking: principles, advances and challenges

(2014) Sheng-You Huang   DRUG DISCOVERY TODAY

Comparative Assessment of Scoring Functions on an Updated Benchmark: 2. Evaluation Methods and General Results

(2014) Yan Li et al.   Journal of Chemical Information and Modeling

Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set

(2014) Yan Li et al.   Journal of Chemical Information and Modeling

Score_set: A CAPRI benchmark for scoring protein complexes

(2014) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

SwarmDock: a server for flexible protein–protein docking

(2013) Mieczyslaw Torchala et al.   BIOINFORMATICS

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

(2013) Iain H Moal et al.   BMC BIOINFORMATICS

Scoring functions for protein–protein interactions

(2013) Iain H Moal et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

ABT-199, a potent and selective BCL-2 inhibitor, achieves antitumor activity while sparing platelets

(2013) Andrew J Souers et al.   NATURE MEDICINE

Binding interface prediction by combining protein-protein docking results

(2013) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improved flexible refinement of protein docking in CAPRI rounds 22-27

(2013) Yang Shen   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Docking, scoring, and affinity prediction in CAPRI

(2013) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2012) Iain H. Moal et al.   BIOINFORMATICS

Computational Drug Design Targeting Protein-Protein Interactions

(2012) Rachelle J. Bienstock   CURRENT PHARMACEUTICAL DESIGN

The Experimental Uncertainty of Heterogeneous Public Ki Data

(2012) Christian Kramer et al.   JOURNAL OF MEDICINAL CHEMISTRY

Overview of theCCP4 suite and current developments

(2011) Martyn D. Winn et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

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

(2011) Iain H. Moal et al.   BIOINFORMATICS

A structure-based benchmark for protein-protein binding affinity

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

Next challenges in protein-protein docking: from proteome to interactome and beyond

(2011) Adrien S.J. Melquiond et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Targeting protein–protein interactions for therapeutic intervention: a challenge for the future

(2010) Giovanna Zinzalla et al.   Future Medicinal 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

Docking and scoring protein interactions: CAPRI 2009

(2010) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-protein docking benchmark version 4.0

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

Comparative Assessment of Scoring Functions on a Diverse Test Set

(2009) Tiejun Cheng et al.   Journal of Chemical Information and Modeling

DOCKGROUND protein-protein docking decoy set

(2008) S. Liu et al.   BIOINFORMATICS

Principles of Protein−Protein Interactions: What are the Preferred Ways For Proteins To Interact?

(2008) Ozlem Keskin et al.   CHEMICAL REVIEWS

Structural basis for distinctive recognition of fibrinogen γC peptide by the platelet integrin αIIbβ3

(2008) Timothy A. Springer et al.   JOURNAL OF CELL BIOLOGY

Estimating the size of the human interactome

(2008) M. P. H. Stumpf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein-protein docking benchmark version 3.0

(2008) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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