ArticleBioinformatics (Oxford, England)2013
FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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
16 citing papers in PubMed.
- Uncovering hidden druggable sites: computational approaches to allosteric and cryptic pocket discovery-from molecular dynamics to AI.Journal of computer-aided molecular design · 2026Review
- Which cryptic sites are feasible drug targets?Drug discovery today · 2024Review
- A comprehensive exploration of the druggable conformational space of protein kinases using AI-predicted structures.PLoS computational biology · 2024Article
- In Silico Methods for Identification of Potential Active Sites of Therapeutic Targets.Molecules (Basel, Switzerland) · 2022Review
- Druggable hot spots in trypanothione reductase: novel insights and opportunities for drug discovery revealed by DRUGpy.Journal of computer-aided molecular design · 2021Article
- Structure-based Druggability Assessment of Anti-virulence Targets from Pseudomonas aeruginosa.Current protein & peptide science · 2019Review
- Exploring the structural origins of cryptic sites on proteins.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Redox-dependent regulation of hepatocyte absent in melanoma 2 inflammasome activation in sterile liver injury in mice.Hepatology (Baltimore, Md.) · 2017Article
- Computational analysis of EBNA1 "druggability" suggests novel insights for Epstein-Barr virus inhibitor design.Journal of computer-aided molecular design · 2016Article
- CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites.Journal of molecular biology · 2016Article
- The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins.Nature protocols · 2015Article
- Theileria parasites secrete a prolyl isomerase to maintain host leukocyte transformation.Nature · 2015Article
- Evidence of conformational selection driving the formation of ligand binding sites in protein-protein interfaces.PLoS computational biology · 2014Article
- Structure-based druggability assessment of the mammalian structural proteome with inclusion of light protein flexibility.PLoS computational biology · 2014Article
- Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology.Molecular informatics · 2014Review
- Structure-based virtual screening for drug discovery: principles, applications and recent advances.Current topics in medicinal chemistry · 2014Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
unlabelledComputational solvent mapping finds binding hot spots, determines their druggability and provides information for drug design. While mapping of a ligand-bound structure yields more accurate results, usually the apo structure serves as the starting point in design. The FTFlex algorithm, implemented as a server, can modify an apo structure to yield mapping results that are similar to those of the respective bound structure. Thus, FTFlex is an extension of our FTMap server, which only considers rigid structures. FTFlex identifies flexible residues within the binding site and determines alternative conformations using a rotamer library. In cases where the mapping results of the apo structure were in poor agreement with those of the bound structure, FTFlex was able to yield a modified apo structure, which lead to improved FTMap results. In cases where the mapping results of the apo and bound structures were in good agreement, no new structure was predicted. AVAILABILITY: FTFlex is freely available as a web-based server at http://ftflex.bu.edu/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.