ArticleProteins2010
Comparison of structure-based and threading-based approaches to protein functional annotation.
Article in Proteins, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 1 of them a synthesis that pooled it.
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Who cites it
24 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Here We Are, But Where Do We Go? A Systematic Review of Crustacean Transcriptomic Studies from 2014-2015.Integrative and comparative biology · 2016Pooled it
- An informatic workflow for the enhanced annotation of excretory/secretory proteins ofComputational and structural biotechnology journal · 2023Article
- Recent Advances in Protein Homology Detection Propelled by Inter-Residue Interaction Map Threading.Frontiers in molecular biosciences · 2021Review
- Computational and Experimental Studies of ADP-Ribosylation.Methods in molecular biology (Clifton, N.J.) · 2017Article
- A web server for analysis, comparison and prediction of protein ligand binding sites.Biology direct · 2016Article
- PDB-Explorer: a web-based interactive map of the protein data bank in shape space.BMC bioinformatics · 2015Article
- On the role of physics and evolution in dictating protein structure and function.Israel journal of chemistry · 2014Article
- Exploring the "dark matter" of a mammalian proteome by protein structure and function modeling.Proteome science · 2013Article
- Interplay of physics and evolution in the likely origin of protein biochemical function.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- eFindSite: improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands.Journal of computer-aided molecular design · 2013Article
- Are predicted protein structures of any value for binding site prediction and virtual ligand screening?Current opinion in structural biology · 2013Review
- IMPORTANCE OF EXCLUDED VOLUME AND HYDRODYNAMIC INTERACTIONS ON MACROMOLECULAR DIFFUSIONQuantum bio-informatics V : proceedings of the quantum bio-informatics 2011, Tokyo University of Science, Japan, 7-12 March 2011. Quantum Bio-Informatics (Conference) (5th : 2011 : Tokyo, Japan) · 2013Article
- FINDSITE(comb): a threading/structure-based, proteomic-scale virtual ligand screening approach.Journal of chemical information and modeling · 2013Article
- Unleashing the power of meta-threading for evolution/structure-based function inference of proteins.Frontiers in genetics · 2013Article
- Rampant exchange of the structure and function of extramembrane domains between membrane and water soluble proteins.PLoS computational biology · 2013Article
- FINDSITE(X): a structure-based, small molecule virtual screening approach with application to all identified human GPCRs.Molecular pharmaceutics · 2012Article
- Speeding up the drug discovery process: structural similarity searches using molecular surfaces.EMBnet.journal · 2012Article
- FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins.BMC bioinformatics · 2011Article
- Protein function prediction: towards integration of similarity metrics.Current opinion in structural biology · 2011Review
- The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement.Journal of structural biology · 2011Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
To exploit the vast amount of sequence information provided by the Genomic revolution, the biological function of these sequences must be identified. As a practical matter, this is often accomplished by functional inference. Purely sequence-based approaches, particularly in the "twilight zone" of low sequence similarity levels, are complicated by many factors. For proteins, structure-based techniques aim to overcome these problems; however, most require high-quality crystal structures and suffer from complex and equivocal relations between protein fold and function. In this study, in extensive benchmarking, we consider a number of aspects of structure-based functional annotation: binding pocket detection, molecular function assignment and ligand-based virtual screening. We demonstrate that protein threading driven by a strong sequence profile component greatly improves the quality of purely structure-based functional annotation in the "twilight zone." By detecting evolutionarily related proteins, it considerably reduces the high false positive rate of function inference derived on the basis of global structure similarity alone. Combined evolution/structure-based function assignment emerges as a powerful technique that can make a significant contribution to comprehensive proteome annotation.
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