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Singh A, Kaushik R, Chaurasia DK, Singh M, Jayaram B. PvP01-DB: computational structural and functional characterization of soluble proteome of PvP01 strain of Plasmodium vivax. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2020:5857404. [PMID: 32542363 PMCID: PMC7296392 DOI: 10.1093/database/baaa036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/07/2020] [Accepted: 04/29/2020] [Indexed: 01/09/2023]
Abstract
Despite Plasmodium vivax being the main offender in the majority of malarial infections, very little information is available about its adaptation and development in humans. Its capability for activating relapsing infections through its dormant liver stage and resistance to antimalarial drugs makes it as one of the major challenges in eradicating malaria. Noting the immediate necessity for the availability of a comprehensive and reliable structural and functional repository for P. vivax proteome, here we developed a web resource for the new reference genome, PvP01, furnishing information on sequence, structure, functions, active sites and metabolic pathways compiled and predicted using some of the state-of-the-art methods in respective fields. The PvP01 web resource comprises organized data on the soluble proteome consisting of 3664 proteins in blood and liver stages of malarial cycle. The current public resources represent only 163 proteins of soluble proteome of PvP01, with complete information about their molecular function, biological process and cellular components. Also, only 46 proteins of P. vivax have experimentally determined structures. In this milieu of extreme scarcity of structural and functional information, PvP01 web resource offers meticulously validated structures of 3664 soluble proteins. The sequence and structure-based functional characterization led to a quantum leap from 163 proteins available presently to whole soluble proteome offered through PvP01 web resource. We believe PvP01 web resource will serve the researchers in identifying novel protein drug targets and in accelerating the development of structure-based new drug candidates to combat malaria. Database Availability: http://www.scfbio-iitd.res.in/PvP01
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Affiliation(s)
- Ankita Singh
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India, 110016.,Centre of Evolution and Medicine, Arizona State University, Life Sciences C, 427 East Tyler Mall, Tempe, AZ 85281, United States
| | - Rahul Kaushik
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India, 110016.,Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Dheeraj Kumar Chaurasia
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India, 110016
| | - Manpreet Singh
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India, 110016
| | - B Jayaram
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India, 110016.,Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, India, 110016.,Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, India, 110016
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Abstract
INTRODUCTION The success of binding site comparisons in drug discovery is based on the recognized fact that many different proteins have similar binding sites. Indeed, binding site comparisons have found many uses in drug development and have the potential to dramatically cut the cost and shorten the time necessary for the development of new drugs. Areas covered: The authors review recent methods for comparing protein binding sites and their use in drug repurposing and polypharmacology. They examine emerging fields including the use of binding site comparisons in precision medicine, the prediction of structured water molecules, the search for targets of natural compounds, and their application in the development of protein-based drugs by loop modeling and for comparison of RNA binding sites. Expert opinion: Binding site comparisons have produced many interesting results in drug development, but relatively little work has been done on protein-protein interaction sites, which are particularly relevant in view of the success of biological drugs. Growth of protein loop modeling for modulating biological drugs is anticipated. The fusion of currently distinct methods for the comparison of RNA and protein binding sites into a single comprehensive approach could allow the search for new selective ribosomal antibiotics and initiate pharmaceutical research into other nucleoproteins.
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Affiliation(s)
- Janez Konc
- a Theory Department , National Institute of Chemistry , Ljubljana , Slovenia.,b Faculty of Pharmacy , University of Ljubljana , Ljubljana , Slovenia.,c Faculty of Mathematics , Natural Sciences and Information Technologies, University of Primorska , Koper , Slovenia.,d Faculty of Chemistry and Chemical Technology , University of Maribor , Maribor , Slovenia
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