ArticleMethods in molecular biology (Clifton, N.J.)2012
Analysis of protein binding sites by computational solvent mapping.
Article in Methods in molecular biology (Clifton, N.J.), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
9 citing papers in PubMed.
- Strategic Template Filtering Accelerates Fragment-Based Peptide Docking.Journal of chemical information and modeling · 2026Article
- Boosting Drug Discovery: Expanding the Applicability of Fragment Dissolved Molecular Dynamics to Accelerate Binding Mode Elucidation.Journal of chemical information and modeling · 2025Article
- Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2.Journal of chemical information and modeling · 2024Article
- Residue-based pharmacophore approaches to study protein-protein interactions.Current opinion in structural biology · 2021Review
- Article
- Protein-protein interaction modulators: advances, successes and remaining challenges.Biophysical reviews · 2019Review
- Protein-protein binding supersites.PLoS computational biology · 2019Article
- Article
- The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins.Nature protocols · 2015Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Computational solvent mapping globally samples the surface of target proteins using molecular probes-small molecules or functional groups-to identify potentially favorable binding positions. The method is based on X-ray and NMR screening studies showing that the binding sites of proteins also bind a large variety of fragment-sized molecules. We have developed the multistage mapping algorithm FTMap (available as a server at http://ftmap.bu.edu/ ) based on the fast Fourier transform (FFT) correlation approach. Identifying regions of low free energy rather than individual low energy conformations, FTMap reproduces the available experimental mapping results. Applications to a variety of proteins show that the probes always cluster in important subsites of the binding site, and the amino acid residues that interact with many probes also bind the specific ligands of the protein. The "consensus" sites at which a number of different probes cluster are likely to be "druggable" sites, capable of binding drug-size ligands with high affinity. Due to its sensitivity to conformational changes, the method can also be used for comparing the binding sites in different structures of a protein.
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Registered trials
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