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Colabind : A Cloud-Based Approach for Prediction of Binding Sites Using Coarse-Grained Simulations with Molecular Probes

Andreev, Georgy (author)
Insilico Med AI Ltd, Masdar City 145748, U Arab Emirates.
Kovalenko, Max (author)
Uppsala universitet,Avdelningen för beräkningsvetenskap
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.
In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 128:13, s. 3211-3219
  • Journal article (peer-reviewed)
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)

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