NDLI: A Protein Relational Database and Protein Family Knowledge Bases to Facilitate Structure-Based Design Analyses

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A Protein Relational Database and Protein Family Knowledge Bases to Facilitate Structure-Based Design Analyses

Content Provider	Scilit
Author	Mobilio, Dominick Walker, Gary Brooijmans, Natasja Nilakantan, Ramaswamy Denny, R. Aldrin Dejoannis, Jason Feyfant, Eric Kowticwar, Rupesh K. Mankala, Jyoti Palli, Satish Punyamantula, Sairam Tatipally, Maneesh John, Reji K. Humblet, Christine
Copyright Year	2010
Description	Journal: Chemical Biology & Drug Design The Protein Data Bank is the most comprehensive source of experimental macromolecular structures. It can, however, be difficult at times to locate relevant structures with the Protein Data Bank search interface. This is particularly true when searching for complexes containing specific interactions between protein and ligand atoms. Moreover, searching within a family of proteins can be tedious. For example, one cannot search for some conserved residue as residue numbers vary across structures. We describe herein three databases, Protein Relational Database, Kinase Knowledge Base, and Matrix Metalloproteinase Knowledge Base, containing protein structures from the Protein Data Bank. In Protein Relational Database, atom-atom distances between protein and ligand have been precalculated allowing for millisecond retrieval based on atom identity and distance constraints. Ring centroids, centroid-centroid and centroid-atom distances and angles have also been included permitting queries for pi-stacking interactions and other structural motifs involving rings. Other geometric features can be searched through the inclusion of residue pair and triplet distances. In Kinase Knowledge Base and Matrix Metalloproteinase Knowledge Base, the catalytic domains have been aligned into common residue numbering schemes. Thus, by searching across Protein Relational Database and Kinase Knowledge Base, one can easily retrieve structures wherein, for example, a ligand of interest is making contact with the gatekeeper residue.
Related Links	http://onlinelibrary.wiley.com/doi/10.1111/j.1747-0285.2010.00994.x/pdf
Ending Page	153
Page Count	12
Starting Page	142
e-ISSN	17470285
DOI	10.1111/j.1747-0285.2010.00994.x
Journal	Chemical Biology & Drug Design
Issue Number	2
Volume Number	76
Language	English
Publisher	Wiley-Blackwell
Publisher Date	2010-07-09
Access Restriction	Open
Subject Keyword	Journal: Chemical Biology & Drug Design Biochemical Research Biochemistry and Molecular Biology Protein Structure Protein‐ligand Interactions Structure‐based Drug Design
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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