Exploring protein-protein interactions using the site-identification by ligand competitive saturation methodology

Identification of Thiourea-Based Inhibitors of the B-Cell Lymphoma 6 BTB Domain via NMR-Based Fragment Screening and Computer-Aided Drug Design

(2018) Huimin Cheng et al.   JOURNAL OF MEDICINAL CHEMISTRY

HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy

(2017) Yumeng Yan et al.   NUCLEIC ACIDS RESEARCH

Modeling protein assemblies: Critical Assessment of Predicted Interactions (CAPRI) 15 years hence.

(2017) Shoshana J. Wodak et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Predicting Protein–Protein Interactions from the Molecular to the Proteome Level

(2016) Ozlem Keskin et al.   CHEMICAL REVIEWS

Structure-based design of N-substituted 1-hydroxy-4-sulfamoyl-2-naphthoates as selective inhibitors of the Mcl-1 oncoprotein

(2016) Maryanna E. Lanning et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Rationally designed BCL6 inhibitors target activated B cell diffuse large B cell lymphoma

(2016) Mariano G. Cardenas et al.   JOURNAL OF CLINICAL INVESTIGATION

Iminoguanidines as Allosteric Inhibitors of the Iron-Regulated Heme Oxygenase (HemO) of Pseudomonas aeruginosa

(2016) Geoffrey A. Heinzl et al.   JOURNAL OF MEDICINAL CHEMISTRY

Protein–protein docking by fast generalized Fourier transforms on 5D rotational manifolds

(2016) Dzmitry Padhorny et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping Functional Group Free Energy Patterns at Protein Occluded Sites: Nuclear Receptors and G-Protein Coupled Receptors

(2015) Sirish Kaushik Lakkaraju et al.   Journal of Chemical Information and Modeling

Pharmacophore Modeling Using Site-Identification by Ligand Competitive Saturation (SILCS) with Multiple Probe Molecules

(2015) Wenbo Yu et al.   Journal of Chemical Information and Modeling

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

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

(2014) Sheng-You Huang   DRUG DISCOVERY TODAY

Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling

(2014) Wenbo Yu et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Inclusion of Multiple Fragment Types in the Site Identification by Ligand Competitive Saturation (SILCS) Approach

(2013) E. Prabhu Raman et al.   Journal of Chemical Information and Modeling

How good is automated protein docking?

(2013) Dima Kozakov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations

(2012) Wenbo Yu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Reproducing Crystal Binding Modes of Ligand Functional Groups Using Site-Identification by Ligand Competitive Saturation (SILCS) Simulations

(2011) E. Prabhu Raman et al.   Journal of Chemical Information and Modeling

SDOCK: A global protein-protein docking program using stepwise force-field potentials

(2011) Changsheng Zhang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2

(2011) Sidhartha Chaudhury et al.   PLoS One

Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library

(2011) Brian G. Pierce et al.   PLoS One

Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation

(2010) Albert Solernou et al.   BMC BIOINFORMATICS

Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation

(2009) Olgun Guvench et al.   PLoS Computational Biology

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation