Exploiting structural information for drug-target assessment

Design of Libraries Targeting Protein-Protein Interfaces

(2013) David Fry et al.   ChemMedChem

One hundred thousand mouse clicks down the road: selected online resources supporting drug discovery collected over a decade

(2013) Bruno O. Villoutreix et al.   DRUG DISCOVERY TODAY

Fast Protein Binding Site Comparison via an Index-Based Screening Technology

(2013) Mathias M. von Behren et al.   Journal of Chemical Information and Modeling

TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins

(2013) Daria B. Kokh et al.   Journal of Chemical Information and Modeling

Subpocket Analysis Method for Fragment-Based Drug Discovery

(2013) Tuomo Kalliokoski et al.   Journal of Chemical Information and Modeling

Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key

(2013) V. Joachim Haupt et al.   PLoS One

Predicting enzymatic function from global binding site descriptors

(2013) Andrea Volkamer et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles

(2012) Zhong-Ru Xie et al.   BIOINFORMATICS

Pharmacophore Fingerprint-Based Approach to Binding Site Subpocket Similarity and Its Application to Bioisostere Replacement

(2012) David J. Wood et al.   Journal of Chemical Information and Modeling

Comparison and Druggability Prediction of Protein–Ligand Binding Sites from Pharmacophore-Annotated Cavity Shapes

(2012) Jérémy Desaphy et al.   Journal of Chemical Information and Modeling

Development of a Rule-Based Method for the Assessment of Protein Druggability

(2012) Emanuele Perola et al.   Journal of Chemical Information and Modeling

ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins

(2012) J. Konc et al.   NUCLEIC ACIDS RESEARCH

Protein flexibility in docking and surface mapping

(2012) Katrina W. Lexa et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Druggability predictions: methods, limitations, and applications

(2012) Xavier Barril   Wiley Interdisciplinary Reviews-Computational Molecular Science

Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction

(2011) Z. Zhang et al.   BIOINFORMATICS

MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories

(2011) Peter Schmidtke et al.   BIOINFORMATICS

Comparative Modeling: The State of the Art and Protein Drug Target Structure Prediction

(2011) Tianyun Liu et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Fragment screening to predict druggability (ligandability) and lead discovery success

(2011) Fredrik N.B. Edfeldt et al.   DRUG DISCOVERY TODAY

DrugPred: A Structure-Based Approach To Predict Protein Druggability Developed Using an Extensive Nonredundant Data Set

(2011) Agata Krasowski et al.   Journal of Chemical Information and Modeling

Pocket-Space Maps To Identify Novel Binding-Site Conformations in Proteins

(2011) Ian R. Craig et al.   Journal of Chemical Information and Modeling

Combining Global and Local Measures for Structure-Based Druggability Predictions

(2011) Andrea Volkamer et al.   Journal of Chemical Information and Modeling

Virtual screening for compounds that mimic protein-protein interface epitopes

(2011) Tim Geppert et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Critical assessment of methods of protein structure prediction (CASP)-round IX

(2011) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

An overview of in silico protein function prediction

(2010) Roy D. Sleator et al.   ARCHIVES OF MICROBIOLOGY

Alignment-Free Ultra-High-Throughput Comparison of Druggable Protein−Ligand Binding Sites

(2010) Nathanaël Weill et al.   Journal of Chemical Information and Modeling

Analyzing the Topology of Active Sites: On the Prediction of Pockets and Subpockets

(2010) Andrea Volkamer et al.   Journal of Chemical Information and Modeling

Drug-like Density: A Method of Quantifying the “Bindability” of a Protein Target Based on a Very Large Set of Pockets and Drug-like Ligands from the Protein Data Bank

(2010) Robert P. Sheridan et al.   Journal of Chemical Information and Modeling

Understanding and Predicting Druggability. A High-Throughput Method for Detection of Drug Binding Sites

(2010) Peter Schmidtke et al.   JOURNAL OF MEDICINAL CHEMISTRY

Using protein-ligand docking to assess the chemical tractability of inhibiting a protein target

(2010) Richard A. Ward   JOURNAL OF MOLECULAR MODELING

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function

(2010) Daniel E. Almonacid et al.   PLoS Computational Biology

Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation

(2009) I. Wallach et al.   BIOINFORMATICS

Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere

(2009) Jian Yu et al.   BIOINFORMATICS

PocketMatch: A new algorithm to compare binding sites in protein structures

(2009) Kalidas Yeturu et al.   BMC BIOINFORMATICS

Fpocket: An open source platform for ligand pocket detection

(2009) Vincent Le Guilloux et al.   BMC BIOINFORMATICS

FINDSITE: a combined evolution/structure-based approach to protein function prediction

(2009) J. Skolnick et al.   BRIEFINGS IN BIOINFORMATICS

Computational Fragment-Based Approach at PDB Scale by Protein Local Similarity

(2009) Fabrice Moriaud et al.   Journal of Chemical Information and Modeling

Identifying and Characterizing Binding Sites and Assessing Druggability

(2009) Thomas A. Halgren   Journal of Chemical Information and Modeling

Tess: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites

(2009) Andrew C. Wallace et al.   PROTEIN SCIENCE

Detection of multiscale pockets on protein surfaces using mathematical morphology

(2009) Takeshi Kawabata   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structure is three to ten times more conserved than sequence-A study of structural response in protein cores

(2009) Kristoffer Illergård et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Form follows function: Shape analysis of protein cavities for receptor-based drug design

(2009) Martin Weisel et al.   PROTEOMICS

Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis

(2009) Sarah L. Kinnings et al.   PLoS Computational Biology

Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites

(2008) R. Najmanovich et al.   BIOINFORMATICS

Biological sequence classification utilizing positive and unlabeled data

(2008) Yuanyuan Xiao et al.   BIOINFORMATICS

How to Measure the Similarity Between Protein Ligand-Binding Sites?

(2008) Esther Kellenberger et al.   Current Computer-Aided Drug Design

Predicting druggable binding sites at the protein–protein interface

(2008) Jonathan C. Fuller et al.   DRUG DISCOVERY TODAY

A structural biology view of target drugability

(2008) Ursula Egner et al.   Expert Opinion on Drug Discovery

A simple and fuzzy method to align and compare druggable ligand-binding sites

(2008) Claire Schalon et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions

(2008) Ryoichi Minai et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS