S No

Cluster

References

Links

1

Anti-Hepatitis

HCV sequence database[i]

European HCV database[ii]

HepSeQ-International Repository of HBV[iii]

HBVRegDb[iv]

 

 

HAVdb[v]

Hepatitis Virus database[vi]

HCVpro[vii]

 

 

 

            HBVdbxv

            ViPR xvi

http://hcv.lanl.gov

http://euhcvdb.ibcp.fr/euHCVdb/

http://www.hepseq.org/Public/Web_Front/main.php

http://lancelot.otago.ac.nz/HBVRegDB/index.php?page=introduction

 



 

http://proline.bic.nus.edu.sg/havdb/index.html

http://s2as02.genes.nig.ac.jp/

http://apps.sanbi.ac.za/hcvpro/

or http://cbrc.kaust.edu.sa/hcvpro/.

 

 

https://hbvdb.ibcp.fr/HBVdb/

http://www.viprbrc.org/brc/home.spg?decorator=flavi_hcv

 

2

Host Defense

 

MHCBN[viii]

MPID[ix]

 

EpiMHCxviii

 

http://www.ncbi.nlm.nih.gov/pubmed/19379493

http://surya.bic.nus.edu.sg/mpid.

http://imed.med.ucm.es/epimhc/

 

3

Anti-Tumor

TumorHPD[x]

TumorHope[xi]

NPACT[xii]

CancerDR[xiii]

CancerPPDxxi

http://crdd.osdd.net/raghava/tumorhpd/.

http://crdd.osdd.net/raghava/tumorhope/.

http://crdd.osdd.net/raghava/npact/

http://crdd.osdd.net/raghava/cancerdr/

http://crdd.osdd.net/raghava/cancerppd/

 

4

Source enrichment

PhytAMP [xiv]

Bactibase[xv]

 

Peptabiotic[xvi]

ASPD[xvii]

http://phytamp.pfba-lab.org.

http://bactibase.pfba-lab-tun.org/main.php

http://peptaibiotics-database.boku.ac.at

http://www.sgi.sscc.ru/mgs/gnw/aspd/.

5

Prediction Enrichment

AMPA[xviii]

UniMap[xix]

Pepserver[xx]

 

 

 

 

PaleAle 4.0[xxi]

CPPsite[xxii]

PepBank[xxiii]

 

http://tcoffee.crg.cat/apps/ampa

http://bioserver-1.bioacademy.gr/Bioserver/UniMaP/

http://bioserver-1.bioacademy.gr/Bioserver/PepServe/.

 

 

http://distillf.ucd.ie/porterpaleale/

http://crdd.osdd.net/raghava/cppsite/.

http://pepbank.mgh.harvard.edu/

 

 

6

Toxicity

ToxinPred[xxiv]

 

PATRN[xxv]

Hemolytik[xxvi]

http://www.imtech.res.in/raghava/toxinpred/index.html

www.patrn.net

 

 

http://crdd.osdd.net/raghava/hemolytik/

 



[i]HCV sequence database: Kuiken C, Yusim K, Boykin L, Richardson R. The Los Alamos HCV Sequence Database.  Bioinformatics(2005), 21(3):379-84.

[ii]http://euhcvdb.ibcp.fr/euHCVdb/

[iii]Gnaneshan S., Ijaz S., Moran J., Ramsay M. and Green J. (2007) HepSEQ: International Public Health Repository for Hepatitis B. Nucleic Acids Res., 35 (Database Issue): D367-70.

[iv]http://lancelot.otago.ac.nz/HBVRegDB/index.php?page=introduction

[v]http://proline.bic.nus.edu.sg/havdb/index.html

[vi]http://s2as02.genes.nig.ac.jp/

[vii]Kwofie SK, Schaefer U, Sundararajan VS, Bajic VB, Christoffels A. HCVpro: Hepatitis C virus protein interaction database. Infect Genet Evol. 2011 Sep 9.

[viii]Bhasin M, Singh H, Raghava GP.MHCBN: a comprehensive database of MHC binding and non-binding peptides.Bioinformatics. 2003 Mar 22;19(5):665-6.

[ix]Govindarajan KR, Kangueane P, Tan TW, Ranganathan S.MPID: MHC-Peptide Interaction Database for sequence-structure-function information on peptides binding to MHC molecules.Bioinformatics. 2003 Jan 22;19(2):309-10.

 

xSharma, A. et al.  Computational approach for designing tumor homing peptides. Sci. Rep. 3, 1607; DOI:10.1038/srep01607 (2013)

[xi]Kapoor P, Singh H, Gautam A, Chaudhary K, Kumar R, Raghava GP.TumorHoPe: a database of tumor homing peptides.PLoS One. 2012;7(4):e35187. doi: 10.1371/journal.pone.0035187.

[xii]Mangal M, Sagar P, Singh H, Raghava GP, Agarwal SM.NPACT: Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database. Nucleic Acids Res. 2013 Jan;41(Database issue):D1124-9. doi: 10.1093/nar/gks1047. Epub 2012 Nov 29.

[xiii]Kumar R, Chaudhary K, Gupta S, Singh H, Kumar S, Gautam A, Kapoor P, Raghava GP.CancerDR: cancer drug resistance database. Sci Rep. 2013;3:1445. doi: 10.1038/srep01445.

[xiv]http://www.ncbi.nlm.nih.gov/pubmed/25270878 Riadh Hammami,Jeannette Ben Hamida,Gérard Vergoten and Ismail Fliss, PhytAMP: a database dedicated to antimicrobial plant peptides Nucl. Acids Res. 2009;37(Database issue)

[xv]Hammami R, Zouhir A, Le Lay C, Ben Hamida J, Fliss I. BACTIBASE second release: a database and tool platform for bacteriocin characterization. BMC Microbiol. 2010 Jan 27;10:22.

[xvi]Stoppacher N, Neumann NK, Burgstaller L, Zeilinger S, Degenkolb T, Brückner H, Schuhmacher R.The comprehensive peptaibiotics database.Chem Biodivers. 2013 May;10(5):734-43. doi: 10.1002/cbdv.201200427.

[xvii]Valuev VP, Afonnikov DA, Ponomarenko MP, Milanesi L, Kolchanov NA.ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro.Nucleic Acids Res. 2002 Jan 1;30(1):200-2.

[xviii]Torrent M, Di Tommaso P, Pulido D, Nogués MV, Notredame C, Boix E, Andreu D. AMPA: an automated web server for prediction of protein antimicrobial regions. Bioinformatics. 2012 Jan 1;28(1):130-1

[xix]Alexandridou A, Tsangaris GT, Vougas K, Nikita K, Spyrou G. UniMaP: finding unique mass and peptide signatures in the human proteome. Bioinformatics. 2009 Nov 15;25(22):3035-7.

[xx]Alexandridou A, Dovrolis N, Tsangaris GT, Nikita K, Spyrou G. PepServe: a web server for peptide analysis, clustering and visualization. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W381-4.

[xxi]Claudio Mirabello and Gianluca Pollastri1.Porter, PaleAle 4.0: high-accuracy prediction of protein secondary structure and relative solvent accessibility. Bioinformatics (2013) 29 (16): 2056-2058.

[xxii]Gautam A, Singh H, Tyagi A, Chaudhary K, Kumar R, Kapoor P, Raghava GP. CPPsite: a curated databse .Published online 2013 May 27. doi:  10.3390/ph6060728

[xxiii]Shtatland T, Guettler D, Kossodo M, Pivovarov M, Weissleder R.PepBank--a database of peptides based on sequence text mining and public peptide data sources.BMC Bioinformatics. 2007 Aug 1;8:280.

[xxiv]Gupta S, Kapoor P, Chaudhary K, Gautam A, Kumar R; Open Source Drug Discovery Consortium, Raghava GP.In silico approach for predicting toxicity of peptides and proteins.PLoS One. 2013 Sep 13;8(9):e73957. doi: 10.1371/journal.pone.0073957. eCollection 2013.

[xxv]Gopinath G, Hari K, Jain R, Mammel MK, Kothary MH, Franco AA, Grim CJ, Jarvis KG, Sathyamoorthy V, Hu L, Datta AR, Patel IR, Jackson SA, Gangiredla J,Kotewicz ML, LeClerc JE, Wekell M, McCardell BA, Solomotis MD, Tall BD.The Pathogen-annotated Tracking Resource Network (PATRN) system: a web-based resource to aid food safety, regulatory science, and investigations of foodborne pathogens and disease.Food Microbiol. 2013 Jun;34(2):303-18. doi: 10.1016/j.fm.2013.01.001. Epub 2013 Jan 23.

[xxvi]Hayer J., Jadeau F., Deléage G., Kay A., Zoulim F., Combet C.HBVdb: a knowledge database for Hepatitis B Virus.


Nucleic Acids Res., 2013, 41:D566-D570.

xxviiGautam A, Chaudhary K, Singh S, Joshi A, Anand P, Tuknait A, Mathur D, Varshney GC, Raghava GP.Hemolytik: a database of experimentally determined hemolytic and non-hemolytic peptides. Nucleic Acids Res. 2014 Jan 1;42(1):D444-9. doi: 10.1093/nar/gkt1008.