VIPERdb2: an enhanced and web API enabled relational database for structural virology.

Authors:
Dr. Mauricio Carrillo-Tripp, PhD
Dr. Mauricio Carrillo-Tripp, PhD
Biomolecular Diversity Laboratory, Cinvestav
Associate Profesor
Computational Biophysics
Irapuato, Guanajuato | México
Ian A Borelli
Ian A Borelli
TPC-6 The Scripps Research Institute
United States
Gabriel Lander
Gabriel Lander
The Scripps Research Institute
Padmaja Natarajan
Padmaja Natarajan
Joint Center for Structural Genomics
John E Johnson
John E Johnson
The Scripps Research Institute
United States
Charles L Brooks
Charles L Brooks
University of Michigan
United States

Nucleic Acids Res 2009 Jan 3;37(Database issue):D436-42. Epub 2008 Nov 3.

Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

VIPERdb (http://viperdb.scripps.edu) is a relational database and a web portal for icosahedral virus capsid structures. Our aim is to provide a comprehensive resource specific to the needs of the virology community, with an emphasis on the description and comparison of derived data from structural and computational analyses of the virus capsids. In the current release, VIPERdb(2), we implemented a useful and novel method to represent capsid protein residues in the icosahedral asymmetric unit (IAU) using azimuthal polar orthographic projections, otherwise known as Phi-Psi (Phi-Psi) diagrams. In conjunction with a new Application Programming Interface (API), these diagrams can be used as a dynamic interface to the database to map residues (categorized as surface, interface and core residues) and identify family wide conserved residues including hotspots at the interfaces. Additionally, we enhanced the interactivity with the database by interfacing with web-based tools. In particular, the applications Jmol and STRAP were implemented to visualize and interact with the virus molecular structures and provide sequence-structure alignment capabilities. Together with extended curation practices that maintain data uniformity, a relational database implementation based on a schema for macromolecular structures and the APIs provided will greatly enhance the ability to do structural bioinformatics analysis of virus capsids.

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkn840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686430PMC

Still can't find the full text of the article?

Sign up to send a request to the authors directly.
January 2009
18 Reads
106 PubMed Central Citations(source)
9.11 Impact Factor

Publication Analysis

Top Keywords

relational database
12
virus capsids
8
database
5
tools applications
4
icosahedral asymmetric
4
applications jmol
4
protein residues
4
residues icosahedral
4
asymmetric unit
4
web-based tools
4
azimuthal polar
4
interactivity database
4
database interfacing
4
iau azimuthal
4
unit iau
4
interfacing web-based
4
residues
4
represent capsid
4
viperdb2 implemented
4
visualize interact
4

References

(Supplied by CrossRef)
Article in Nucleic Acids Research
Shepherd et al.
Nucleic Acids Research 2006
Article in Journal of Virology
Reddy et al.
Journal of Virology 2001
Article in Nature reviews. Microbiology
Natarajan et al.
Nature reviews. Microbiology 2005
Article in Proteins
Shepherd et al.
Proteins 2005
Article in Journal of molecular biology
Damodaran et al.
Journal of molecular biology 2002
Article in Proteins
Carrillo-Tripp et al.
Proteins 2008
Article in Nucleic Acids Research
Berman et al.
Nucleic Acids Research 2000
Article in Journal of computational chemistry
Journal of computational chemistry 1983
Article in Journal of molecular biology
O'Sullivan et al.
Journal of molecular biology 2004
Article in Bioinformatics
Gille et al.
Bioinformatics 2001
Article in Journal of Applied Crystallography
Journal of Applied Crystallography 1991

Similar Publications

Cryptic sequence features in the active postmortem transcriptome.

BMC Genomics 2018 Sep 14;19(1):675. Epub 2018 Sep 14.

City of Hope, Information Sciences - Beckman Research Institute, 4920 Rivergrade Rd., Irwindale, CA, 91706, USA.

Background: Our previous study found that more than 500 transcripts significantly increased in abundance in the zebrafish and mouse several hours to days postmortem relative to live controls. The current literature suggests that most mRNAs are post-transcriptionally regulated in stressful conditions. We rationalized that the postmortem transcripts must contain sequence features (3- to 9- mers) that are unique from those in the rest of the transcriptome and that these features putatively serve as binding sites for proteins and/or non-coding RNAs involved in post-transcriptional regulation. Read More

View Article
September 2018
42 Reads
3.99 Impact Factor

Direct observation of Medicaid beneficiary attempts to fill prescriptions for nicotine replacement medications.

J Am Pharm Assoc (2003) 2018 Jul - Aug;58(4):432-437. Epub 2018 Apr 22.

Objectives: Although many states have expanded Medicaid coverage of cessation medications, utilization remains low. Anecdotal reports suggest that beneficiaries are at times denied coverage of cessation medications at the pharmacy counter. We conducted an observational community-wide case study of Medicaid beneficiary attempts to fill over-the-counter nicotine replacement therapy at pharmacies. Read More

View Article
April 2018
40 Reads

Chemical reaction dynamics.

Chem Soc Rev 2017 Dec;46(24):7481-7482

State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.

View Article
December 2017
37 Reads
33.38 Impact Factor

Activity of 2-(quinolin-4-yloxy)acetamides in Mycobacterium tuberculosis clinical isolates and identification of their molecular target by whole-genome sequencing.

Int J Antimicrob Agents 2018 Mar 23;51(3):378-384. Epub 2017 Aug 23.

Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Av. Ipiranga 6681 - Prédio 92A Tecnopuc, Porto Alegre, RS 90619-900, Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, Brazil.

The 2-(quinolin-4-yloxy)acetamides (QOAs) have been reported to be promising molecules for tuberculosis treatment. Recent studies demonstrated their potent antimycobacterial activity, biological stability and synergism with rifampicin. The identification of the molecular target is an essential step towards the development of a novel drug candidate. Read More

View Article
March 2018
62 Reads
2 PubMed Central Citations(source)
4.30 Impact Factor

Covalent inhibition of protein tyrosine phosphatases.

Mol Biosyst 2017 Jun;13(7):1257-1279

Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907, USA.

Protein tyrosine phosphatases (PTPs) are a large family of 107 signaling enzymes that catalyze the hydrolytic removal of phosphate groups from tyrosine residues in a target protein. The phosphorylation status of tyrosine residues on proteins serve as a ubiquitous mechanism for cellular signal transduction. Aberrant function of PTPs can lead to many human diseases, such as diabetes, obesity, cancer, and autoimmune diseases. Read More

View Article
June 2017
57 Reads