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

Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks

(2015) John A. Gerlt et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

mFASD: a structure-based algorithm for discriminating different types of metal-binding sites

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PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment

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GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions: Fig. 1.

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DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe

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Predicting protein functions using incomplete hierarchical labels

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Template-based prediction of protein function

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Constructing Query-Driven Dynamic Machine Learning Model With Application to Protein-Ligand Binding Sites Prediction

(2015) Dong-Jun Yu et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

Identification of Protein–Ligand Binding Sites by the Level-Set Variational Implicit-Solvent Approach

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Improvements, trends, and new ideas in molecular docking: 2012-2013 in review

(2015) Elizabeth Yuriev et al.   JOURNAL OF MOLECULAR RECOGNITION

Structural Bioinformatics Inspection of neXtProt PE5 Proteins in the Human Proteome

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The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins

(2015) Dima Kozakov et al.   Nature Protocols

IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences: Figure 1.

(2015) Liam J. McGuffin et al.   NUCLEIC ACIDS RESEARCH

CATH FunFHMMer web server: protein functional annotations using functional family assignments

(2015) Sayoni Das et al.   NUCLEIC ACIDS RESEARCH

INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity

(2015) Damiano Piovesan et al.   NUCLEIC ACIDS RESEARCH

SIFTER search: a web server for accurate phylogeny-based protein function prediction

(2015) Sayed M. Sahraeian et al.   NUCLEIC ACIDS RESEARCH

PLIP: fully automated protein–ligand interaction profiler

(2015) Sebastian Salentin et al.   NUCLEIC ACIDS RESEARCH

Functional characterization of glutathione S-transferases associated with insecticide resistance in Tetranychus urticae

(2015) Nena Pavlidi et al.   PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY

Combining features in a graphical model to predict protein binding sites

(2015) Torsten Wierschin et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

(2015) Tiffany B. Taylor et al.   SCIENCE

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

(2015) Radoslav Krivák et al.   Journal of Cheminformatics

GASS: identifying enzyme active sites with genetic algorithms

(2014) Sandro C. Izidoro et al.   BIOINFORMATICS

LigDig: a web server for querying ligand–protein interactions

(2014) Jonathan C. Fuller et al.   BIOINFORMATICS

Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0

(2014) Xiaolei Zhu et al.   BIOINFORMATICS

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

(2014) Peng Chen et al.   BMC BIOINFORMATICS

Extended Graph-Based Models for Enhanced Similarity Search in Cavbase

(2014) Timo Krotzky et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Scents and sense:In silicoperspectives on olfactory receptors

(2014) Charleen G. Don et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

(2014) Lim Heo et al.   NUCLEIC ACIDS RESEARCH

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

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

(2013) Jianyi Yang et al.   BIOINFORMATICS

Fifty-five years of enzyme classification: advances and difficulties

(2013) Andrew G. McDonald et al.   FEBS Journal

COOH-terminal collagen Q (COLQ) mutants causing human deficiency of endplate acetylcholinesterase impair the interaction of ColQ with proteins of the basal lamina

(2013) Juan Arredondo et al.   HUMAN GENETICS

Designing Template-Free Predictor for Targeting Protein-Ligand Binding Sites with Classifier Ensemble and Spatial Clustering

(2013) Dong-Jun Yu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Human Cytochrome P450 1A1 Structure and Utility in Understanding Drug and Xenobiotic Metabolism

(2013) Agnes A. Walsh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Encoding Protein–Ligand Interaction Patterns in Fingerprints and Graphs

(2013) Jérémy Desaphy et al.   Journal of Chemical Information and Modeling

Two-dimensional replica-exchange method for predicting protein-ligand binding structures

(2013) Hironori Kokubo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Protein-specific force field derived from the fragment molecular orbital method can improve protein-ligand binding interactions

(2013) Le Chang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A large-scale evaluation of computational protein function prediction

(2013) Predrag Radivojac et al.   NATURE METHODS

LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites

(2013) Zhong-Ru Xie et al.   NUCLEIC ACIDS RESEARCH

The FunFOLD2 server for the prediction of protein–ligand interactions

(2013) Daniel B. Roche et al.   NUCLEIC ACIDS RESEARCH

The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes

(2013) Nicholas Furnham et al.   NUCLEIC ACIDS RESEARCH

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

SiteComp: a server for ligand binding site analysis in protein structures

(2012) Yingjie Lin et al.   BIOINFORMATICS

Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study

(2012) Jose C A Santos et al.   BMC BIOINFORMATICS

Structure and evolution of barley powdery mildew effector candidates

(2012) Carsten Pedersen et al.   BMC GENOMICS

A scalable and accurate method for classifying protein–ligand binding geometries using a MapReduce approach

(2012) T. Estrada et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Calciomics: integrative studies of Ca2+-binding proteins and their interactomes in biological systems

(2012) Yubin Zhou et al.   Metallomics

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

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

BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions

(2012) Jianyi Yang et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Ambrish Roy et al.   NUCLEIC ACIDS RESEARCH

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013

(2012) Janna Hastings et al.   NUCLEIC ACIDS RESEARCH

FunFOLDQA: A Quality Assessment Tool for Protein-Ligand Binding Site Residue Predictions

(2012) Daniel B. Roche et al.   PLoS One

FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins

(2011) Daniel B Roche et al.   BMC BIOINFORMATICS

Proteogenomics and in silico structural and functional annotation of the barley powdery mildew Blumeria graminis f. sp. hordei

(2011) Laurence V. Bindschedler et al.   METHODS

The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction

(2011) D. B. Roche et al.   NUCLEIC ACIDS RESEARCH

Surface-based protein binding pocket similarity

(2011) Russell Spitzer et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of ligand-binding residue predictions in CASP9

(2011) Tobias Schmidt et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The binding site distance test score: a robust method for the assessment of predicted protein binding sites

(2010) Daniel B. Roche et al.   BIOINFORMATICS

ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment

(2010) Janez Konc et al.   BIOINFORMATICS

Active site prediction using evolutionary and structural information

(2010) Sriram Sankararaman et al.   BIOINFORMATICS

An interaction-motif-based scoring function for protein-ligand docking

(2010) Zhong-Ru Xie et al.   BMC BIOINFORMATICS

3DLigandSite: predicting ligand-binding sites using similar structures

(2010) Mark N. Wass et al.   NUCLEIC ACIDS RESEARCH

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

(2010) H. Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

WSsas: a web service for the annotation of functional residues through structural homologues

(2009) D. Talavera et al.   BIOINFORMATICS

Evolutionary Trace Annotation of Protein Function in the Structural Proteome

(2009) Serkan Erdin et al.   JOURNAL OF MOLECULAR BIOLOGY

INTREPID: a web server for prediction of functionally important residues by evolutionary analysis

(2009) S. Sankararaman et al.   NUCLEIC ACIDS RESEARCH

SITEHOUND-web: a server for ligand binding site identification in protein structures

(2009) M. Hernandez et al.   NUCLEIC ACIDS RESEARCH

Mapping of ligand-binding cavities in proteins

(2009) C. David Andersson et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-binding site prediction based on three-dimensional protein modeling

(2009) Mina Oh et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of ligand binding residue predictions in CASP8

(2009) Gonzalo López et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

ConFunc—functional annotation in the twilight zone

(2008) Mark N. Wass et al.   BIOINFORMATICS

Protein-ligand interaction prediction: an improved chemogenomics approach

(2008) Laurent Jacob et al.   BIOINFORMATICS

KEGG Atlas mapping for global analysis of metabolic pathways

(2008) S. Okuda et al.   NUCLEIC ACIDS RESEARCH

Effects of CYP inducers and inhibitors on the pharmacokinetics of intravenous theophylline in rats: involvement of CYP1A1/2 in the formation of 1,3-DMU

(2007) Kyung H. Yang et al.   JOURNAL OF PHARMACY AND PHARMACOLOGY