P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure

An Augmented Pocketome: Detection and Analysis of Small-Molecule Binding Pockets in Proteins of Known 3D Structure

(2018) Raghu Bhagavat et al.   STRUCTURE

Protein–Ligand Scoring with Convolutional Neural Networks

(2017) Matthew Ragoza et al.   Journal of Chemical Information and Modeling

TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets

(2017) Antonia Stank et al.   NUCLEIC ACIDS RESEARCH

Unveiling a novel transient druggable pocket in BACE-1 through molecular simulations: Conformational analysis and binding mode of multisite inhibitors

(2017) Ornella Di Pietro et al.   PLoS One

Conformational diversity analysis reveals three functional mechanisms in proteins

(2017) Alexander Miguel Monzon et al.   PLoS Computational Biology

Can We Rely on Computational Predictions To Correctly Identify Ligand Binding Sites on Novel Protein Drug Targets? Assessment of Binding Site Prediction Methods and a Protocol for Validation of Predicted Binding Sites

(2016) Neal K. Broomhead et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

Comparison ofin silicotools for binding site prediction applied for structure-based design of autolysin inhibitors

(2016) T. Tibaut et al.   SAR AND QSAR IN ENVIRONMENTAL RESEARCH

bSiteFinder, an improved protein-binding sites prediction server based on structural alignment: more accurate and less time-consuming

(2016) Jun Gao et al.   Journal of Cheminformatics

Mapping the 3D structures of small molecule binding sites

(2016) Joshua Meyers et al.   Journal of Cheminformatics

Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods

(2015) Daniel Roche et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Graph-Based Clustering of Predicted Ligand-Binding Pockets on Protein Surfaces

(2015) Jennifer Degac et al.   Journal of Chemical Information and Modeling

PockDrug-Server: a new web server for predicting pocket druggability on holo and apo proteins

(2015) Hiba Abi Hussein et al.   NUCLEIC ACIDS RESEARCH

Improving protein-ligand binding site prediction accuracy by classification of inner pocket points using local features

(2015) Radoslav Krivák et al.   Journal of Cheminformatics

Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets

(2015) Wei P. Feinstein et al.   Journal of Cheminformatics

LigandRFs: random forest ensemble to identify ligand-binding residues from sequence information alone

(2014) Peng Chen et al.   BMC BIOINFORMATICS

Computational tools for designing and engineering enzymes

(2014) Jiri Damborsky et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Structure-Based Virtual Screening for Drug Discovery: Principles, Applications and Recent Advances

(2014) Evanthia Lionta et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Facing the Challenges of Structure-Based Target Prediction by Inverse Virtual Screening

(2014) Karen T. Schomburg et al.   Journal of Chemical Information and Modeling

sc-PDB: a 3D-database of ligandable binding sites—10 years on

(2014) Jérémy Desaphy et al.   NUCLEIC ACIDS RESEARCH

GalaxySite: ligand-binding-site prediction by using molecular docking

(2014) Lim Heo et al.   NUCLEIC ACIDS RESEARCH

Allosite: a method for predicting allosteric sites

(2013) Wenkang Huang et al.   BIOINFORMATICS

Protein–ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment

(2013) Jianyi Yang et al.   BIOINFORMATICS

Binding site comparison for function prediction and pharmaceutical discovery

(2013) Janez Konc et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity

(2013) Hui Sun Lee et al.   Journal of Chemical Information and Modeling

eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands

(2013) Michal Brylinski et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

A Simple Atomic-Level Hydrophobicity Scale Reveals Protein Interfacial Structure

(2013) Lauren H. Kapcha et al.   JOURNAL OF MOLECULAR BIOLOGY

Assessment of ligand binding site predictions in CASP10

(2013) Tiziano Gallo Cassarino et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Protein Model Portal—a comprehensive resource for protein structure and model information

(2013) Juergen Haas et al.   Database-The Journal of Biological Databases and Curation

Exploring the Composition of Protein-Ligand Binding Sites on a Large Scale

(2013) Nickolay A. Khazanov et al.   PLoS Computational Biology

Pocket-Based Drug Design: Exploring Pocket Space

(2012) Xiliang Zheng et al.   AAPS Journal

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

(2012) Zhong-Ru Xie et al.   BIOINFORMATICS

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

COFACTOR: an accurate comparative algorithm for structure-based protein function annotation

(2012) Ambrish Roy et al.   NUCLEIC ACIDS RESEARCH

FTSite: high accuracy detection of ligand binding sites on unbound protein structures

(2011) Chi-Ho Ngan et al.   BIOINFORMATICS

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

Structure-based druggability assessment—identifying suitable targets for small molecule therapeutics

(2011) Eric B Fauman et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Structure-based systems biology for analyzing off-target binding

(2011) Lei Xie et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A De Novo Protein Binding Pair By Computational Design and Directed Evolution

(2011) John Karanicolas et al.   MOLECULAR CELL

Improved Prediction of Protein Ligand-Binding Sites Using Random Forests

(2011) Zhijun Qiu et al.   PROTEIN AND PEPTIDE LETTERS

A Critical Comparative Assessment of Predictions of Protein-Binding Sites for Biologically Relevant Organic Compounds

(2011) Ke Chen et al.   STRUCTURE

MSPocket: an orientation-independent algorithm for the detection of ligand binding pockets

(2010) Hongbo Zhu et al.   BIOINFORMATICS

In Silico Prediction of Binding Sites on Proteins

(2010) Simon Leis et al.   CURRENT MEDICINAL CHEMISTRY

Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery

(2010) Stéphanie Pérot et al.   DRUG DISCOVERY TODAY

Large-Scale Comparison of Four Binding Site Detection Algorithms

(2010) Peter Schmidtke 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

LIBRUS: combined machine learning and homology information for sequence-based ligand-binding residue prediction

(2009) C. Kauffman et al.   BIOINFORMATICS

EasyMIFs and SiteHound: a toolkit for the identification of ligand-binding sites in protein structures

(2009) Dario Ghersi 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

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

Identifying and Characterizing Binding Sites and Assessing Druggability

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

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

(2009) John A. Capra et al.   PLoS Computational Biology

Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures

(2008) Mizuki Morita et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations

(2002) Buyong Ma et al.   PROTEIN SCIENCE