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Assessment of ligand‐binding residue predictions in CASP9

https://doi.org/10.1002/prot.23174
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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The prediction of protein function at CASP6
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A method for localizing ligand binding pockets in protein structures
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Assessment of predictions submitted for the CASP7 function prediction category
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Prediction of ligand binding sites using homologous structures and conservation at CASP8
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Assessment of ligand binding residue predictions in CASP8
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Protein‐binding site prediction based on three‐dimensional protein modeling
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LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins
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A Critical Assessment of Docking Programs and Scoring Functions
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Benchmarking Sets for Molecular Docking
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Prediction of Protein−Ligand Interactions. Docking and Scoring: Successes and Gaps
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Virtual screening of chemical libraries
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A method to predict functional residues in proteins
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Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions
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A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
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Structure-based function prediction: approaches and applications
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ConSeq: the identification of functionally and structurally important residues in protein sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btl104openalex-snapshot
Phylogeny-independent detection of functional residues
inferredcites →https://doi.org/10.1093/bioinformatics/btm626openalex-snapshot
Prediction of protein functional residues from sequence by probability density estimation
inferredcites →https://doi.org/10.1093/bioinformatics/btq006openalex-snapshot
PSiFR: an integrated resource for prediction of protein structure and function
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OpenStructure: a flexible software framework for computational structural biology
inferredcites →https://doi.org/10.1093/bioinformatics/btq543openalex-snapshot
The binding site distance test score: a robust method for the assessment of predicted protein binding sites
inferredcites →https://doi.org/10.1093/nar/gkl971openalex-snapshot
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
inferredcites →https://doi.org/10.1093/nar/gkm297openalex-snapshot
firestar--prediction of functionally important residues using structural templates and alignment reliability
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siteFiNDER 3D: a web-based tool for predicting the location of functional sites in proteins
inferredcites →https://doi.org/10.1093/nar/gkp281openalex-snapshot
SITEHOUND-web: a server for ligand binding site identification in protein structures
inferredcites →https://doi.org/10.1093/nar/gkq1020openalex-snapshot
Ongoing and future developments at the Universal Protein Resource
inferredcites →https://doi.org/10.1093/nar/gkq406openalex-snapshot
3DLigandSite: predicting ligand-binding sites using similar structures
inferredcites →https://doi.org/10.1186/1472-6807-6-19openalex-snapshot
LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation.
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Individual Comparisons by Ranking Methods
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Assessment of template based protein structure predictions in CASP9
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Additional file 1 of EDock: blind protein–ligand docking by replica-exchange monte carlo simulation
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