2020
DOI: 10.1101/2020.02.02.931436
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Algorithm for Extraction of Sub-Structure from Co-Crystallized PDB Ligand for Selective Targeting

Abstract: An algorithm has been introduced for extraction of sub-structure from co-crystallized ligand of complex PDB file. Algorithm utilized location of atoms in 3D domain of complex of ligand & protein. It processed relative positioning of atoms for demarcation of influential part of ligand, which can provide potency to that ligand for binding with specific binding pocket of protein. Algorithm was validated with ligands cocrystallized with enzymes of different classes. Extracted sub-structures were validated (via evi… Show more

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Cited by 2 publications
(3 citation statements)
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“…The RUMSSA approach was used to manually extract substructures from PDB data including co-crystallized ligands (rcsb.org). Details about the RUMMSA algorithm implemented, can be accessed from the literature 'BioRxiv 2020.02.02.931436' [11].…”
Section: Methods To Extract Sub-structurementioning
confidence: 99%
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“…The RUMSSA approach was used to manually extract substructures from PDB data including co-crystallized ligands (rcsb.org). Details about the RUMMSA algorithm implemented, can be accessed from the literature 'BioRxiv 2020.02.02.931436' [11].…”
Section: Methods To Extract Sub-structurementioning
confidence: 99%
“…Although the RUMSSA method is detailed in publication [11], but it can be summarised as follows: RUMSSA (Relative Unified Mechanical Skill Score of Atom) is a method that can determine a ligand's substructure from a PDB file comprising two molecules (Protein-Ligand) interacting. Calibration is required for each complex.…”
Section: Algorithm Briefmentioning
confidence: 99%
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