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Colabind :
Colabind : A Cloud-Based Approach for Prediction of Binding Sites Using Coarse-Grained Simulations with Molecular Probes
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- Andreev, Georgy (author)
- Insilico Med AI Ltd, Masdar City 145748, U Arab Emirates.
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- Kovalenko, Max (author)
- Uppsala universitet,Avdelningen för beräkningsvetenskap
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- Bozdaganyan, Marine E. (author)
- Shenzhen MSU BIT Univ, Fac Biol, Shenzhen 518172, Peoples R China.
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- Orekhov, Philipp S. (author)
- Shenzhen MSU BIT Univ, Fac Biol, Shenzhen 518172, Peoples R China.
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Insilico Med AI Ltd, Masdar City 145748, U Arab Emirates Avdelningen för beräkningsvetenskap (creator_code:org_t)
- American Chemical Society (ACS), 2024
- 2024
- English.
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In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 128:13, s. 3211-3219
- Related links:
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Subject headings
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- Binding site prediction is a crucial step in understanding protein-ligand and protein-protein interactions (PPIs) with broad implications in drug discovery and bioinformatics. This study introduces Colabind, a robust, versatile, and user-friendly cloud-based approach that employs coarse-grained molecular dynamics simulations in the presence of molecular probes, mimicking fragments of drug-like compounds. Our method has demonstrated high effectiveness when validated across a diverse range of biological targets spanning various protein classes, successfully identifying orthosteric binding sites, as well as known druggable allosteric or PPI sites, in both experimentally determined and AI-predicted protein structures, consistently placing them among the top-ranked sites. Furthermore, we suggest that careful inspection of the identified regions with a high affinity for specific probes can provide valuable insights for the development of pharmacophore hypotheses. The approach is available at https://github.com/porekhov/CG_probeMD
Subject headings
- NATURVETENSKAP -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
Publication and Content Type
- ref (subject category)
- art (subject category)
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