Algorithm for Extraction of Sub-Structure from Co-Crystallized PDB Ligand for Selective Targeting

Prakash, Om

doi:10.1101/2020.02.02.931436

Cited by 2 publications

(3 citation statements)

References 8 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…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%

“…The RUMSSA (Relative Unified Mechanical Skill Score of Atom) technique, in addition to existing methodologies, uses X-ray crystallographic complex structure to identify potentially influential sub-structure(s) from ligand. The position of atoms in the 3D domain of a ligand-protein combination was thought to contain high selectivity information [11]. As a result, mechanical transformations of relative positioning can be employed to gather data for identifying the ligand's influential component inside the complex system of a certain protein binding pocket.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

CoSSDb: A Database of Co-crystallized Ligand Sub-structures for Anticancer Lead Designing & Optimization

Prakash¹,

Khan²

2022

Proceedings of the Conference BioSangam 2022: Emerging Trends in Biotechnology (BIOSANGAM 2022)

Self Cite

View full text Add to dashboard Cite

The Discovery of the novel optimized structures of small molecules for selective targeting is one of the challenging tasks in drug designing. Bioisosteres are the key components of the lead compound, which provide hidden power to the compound scaffold for selective targeting. We are presenting a database, named CoSSDb which stands for Co-crystallized Sub-Structure Database. The CoSSDb contains ligand sub-structures as possible bioisosteres. extracted from PDB files, available in Protein Data Bank. Sub-structures were extracted through an algorithm, which utilizes the location of atoms in the 3D domain of the complex ligand & protein. It processes the relative positioning of atoms for demarcation of the influential part of the ligand, which interacts with macromolecule and provides potency to that ligand for binding with a specific binding pocket of the protein. The algorithm was used to extract sub-structures from the ligands co-crystallized with proteins involved in cancer. About 7721 x-ray crystallography PDB files were processed, and 654 non-redundant substructures were identified. These sub-structures will be useful during designing & optimization of novel ligands for selective targets. The database is freely accessible at ‘https://opticket49.wixsite.com/substructdb’.

show abstract

Section: Methods To Extract Sub-structurementioning

confidence: 99%

Section: Algorithm Briefmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation