VIPERdb v3.0: a structure-based data analytics platform for viral capsids

被引：51

作者：

Montiel-Garcia, Daniel ^{[1
,2
,3
,4
]}

Santoyo-Rivera, Nelly ^{[2
,3
,4
]}

Phuong Ho ^{[1
,9
]}

Carrillo-Tripp, Mauricio ^{[5
]}

Brooks, Charles L., III ^{[6
,7
,8
]}

Johnson, John E. ^{[1
]}

Reddy, Vijay S. ^{[1
]}

机构：

[1] Scripps Res Inst, Dept Integrat Struct & Computat Biol, La Jolla, CA 92037 USA

[2] Tecnol Nacl Mexico, Dept Comp Syst, Guanajuato, Mexico

[3] Tecnol Nacl Mexico, Dept Informat Technol, Guanajuato, Mexico

[4] Inst Tecnol Super Irapuato, Guanajuato, Mexico

[5] Ctr Invest & Estudios Avanzados, Unidad Monterrey, Biomol Divers Lab, Via Conocimiento 201,Parque PIIT, Apodaca 66600, Nuevo Leon, Mexico

[6] Univ Michigan, Dept Computat Med & Bioinformat, Ann Arbor, MI 48109 USA

[7] Univ Michigan, Dept Chem, Ann Arbor, MI 48109 USA

[8] Univ Michigan, Dept Biophys, Ann Arbor, MI 48109 USA

[9] Univ Calif San Diego, Dept Bioengn, 9500 Gilman Dr, La Jolla, CA 92039 USA

来源：

NUCLEIC ACIDS RESEARCH | 2021年 / 49卷 / D1期

关键词：

D O I：

10.1093/nar/gkaa1096

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

VIrus Particle ExploreR data base (VIPERdb) (http: //viperdb.scripps.edu) is a curated repository of virus capsid structures and a database of structure-derived data along with various virus specific information. VIPERdb has been continuously improved for over 20 years and contains a number of virus structure analysis tools. The release of VIPERdb v3.0 contains new structure-based data analytics tools like Multiple Structure-based and Sequence Alignment (MSSA) to identify hot-spot residues within a selected group of structures and an anomaly detection application to analyze and curate the structurederived data within individual virus families. At the time of this writing, there are 931 virus structures from 62 different virus families in the database. Significantly, the new release also contains a standalone database called 'Virus World database' (VWdb) that comprises all the characterized viruses (similar to 181 000) known to date, gathered from ICTVdb and NCBI, and their capsid protein sequences, organized according to their virus taxonomy with links to known structures in VIPERdb and PDB. Moreover, the newrelease of VIPERdb includes a service-oriented data engine to handle all the data access requests and provides an interface for futuristic data analytics using machine leaning applications.

引用

页码：D809 / D816

页数：8

共 12 条

[1]

Acland A, 2013, NUCLEIC ACIDS RES, V41, pD8, DOI [10.1093/nar/gks1189, 10.1093/nar/gkx1095, 10.1093/nar/gkq1172]

[2] 50 years of the International Committee on Taxonomy of Viruses: progress and prospects [J].

Adams, Michael J. ;

Lefkowitz, Elliot J. ;

King, Andrew M. Q. ;

Harrach, Balazs ;

Harrison, Robert L. ;

Knowles, Nick J. ;

Kropinski, Andrew M. ;

Krupovic, Mart ;

Kuhn, Jens H. ;

Mushegian, Arcady R. ;

Nibert, Max L. ;

Sabanadzovic, Sead ;

Sanfacon, Helene ;

Siddell, Stuart G. ;

Simmonds, Peter ;

Varsani, Arvind ;

Zerbini, Francisco Murilo ;

Orton, Richard J. ;

Smith, Donald B. ;

Gorbalenya, Alexander E. ;

Davison, Andrew J. .

ARCHIVES OF VIROLOGY, 2017, 162 (05) :1441-1446

[3] TexMol: Interactive visual exploration of large flexible multi-component molecular complexes [J].

Bajaj, C ;

Djeu, P ;

Siddavanahalli, V ;

Thane, A .

IEEE VISUALIZATION 2004, PROCEEEDINGS, 2004, :243-250

[4] UniProt: a worldwide hub of protein knowledge [J].

Bateman, Alex ;

Martin, Maria-Jesus ;

Orchard, Sandra ;

Magrane, Michele ;

Alpi, Emanuele ;

Bely, Benoit ;

Bingley, Mark ;

Britto, Ramona ;

Bursteinas, Borisas ;

Busiello, Gianluca ;

Bye-A-Jee, Hema ;

Da Silva, Alan ;

De Giorgi, Maurizio ;

Dogan, Tunca ;

Castro, Leyla Garcia ;

Garmiri, Penelope ;

Georghiou, George ;

Gonzales, Daniel ;

Gonzales, Leonardo ;

Hatton-Ellis, Emma ;

Ignatchenko, Alexandr ;

Ishtiaq, Rizwan ;

Jokinen, Petteri ;

Joshi, Vishal ;

Jyothi, Dushyanth ;

Lopez, Rodrigo ;

Luo, Jie ;

Lussi, Yvonne ;

MacDougall, Alistair ;

Madeira, Fabio ;

Mahmoudy, Mahdi ;

Menchi, Manuela ;

Nightingale, Andrew ;

Onwubiko, Joseph ;

Palka, Barbara ;

Pichler, Klemens ;

Pundir, Sangya ;

Qi, Guoying ;

Raj, Shriya ;

Renaux, Alexandre ;

Lopez, Milagros Rodriguez ;

Saidi, Rabie ;

Sawford, Tony ;

Shypitsyna, Aleksandra ;

Speretta, Elena ;

Turner, Edward ;

Tyagi, Nidhi ;

Vasudev, Preethi ;

Volynkin, Vladimir ;

Wardell, Tony .

NUCLEIC ACIDS RESEARCH, 2019, 47 (D1) :D506-D515

[5] The Protein Data Bank [J].

Berman, HM ;

Westbrook, J ;

Feng, Z ;

Gilliland, G ;

Bhat, TN ;

Weissig, H ;

Shindyalov, IN ;

Bourne, PE .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242

[6] VIPERdb2: an enhanced and web API enabled relational database for structural virology [J].

Carrillo-Tripp, Mauricio ;

Shepherd, Craig M. ;

Borelli, Ian A. ;

Venkataraman, Sangita ;

Lander, Gabriel ;

Natarajan, Padmaja ;

Johnson, John E. ;

Brooks, Charles L., III ;

Reddy, Vijay S. .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D436-D442

[7] VIPERdb: A Tool for Virus Research [J].

Ho, Phuong T. ;

Montiel-Garcia, Daniel J. ;

Wong, Jonathan. J. ;

Carrillo-Tripp, Mauricio ;

Brooks, Charles L., III ;

Johnson, John E. ;

Reddy, Vijay S. .

ANNUAL REVIEW OF VIROLOGY, VOL 5, 2018, 5 :477-488

[8] UCSF chimera - A visualization system for exploratory research and analysis [J].

Pettersen, EF ;

Goddard, TD ;

Huang, CC ;

Couch, GS ;

Greenblatt, DM ;

Meng, EC ;

Ferrin, TE .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 2004, 25 (13) :1605-1612

[9] Virus Particle Explorer (VIPER), a Website for virus capsid structures and their computational analyses [J].

Reddy, VS ;

Natarajan, P ;

Okerberg, B ;

Li, K ;

Damodaran, KV ;

Morton, RT ;

Brooks, C ;

Johnson, JE .

JOURNAL OF VIROLOGY, 2001, 75 (24) :11943-11947

[10] Calculating and scoring high quality multiple flexible protein structure alignments [J].

Ritchie, David W. .

BIOINFORMATICS, 2016, 32 (17) :2650-2658

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