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Databases

Collection and compilation of biological data from literature and other resources is one of the major goals for bioinformaticians. These databases are based for computational biology. Our group have developed various databases to maintain wide range of biological data. Following is list of major databases.

Biological and Medical Databases (Raghava's Group)

  1. AntigenDB: an immunoinformatics database of pathogen antigens.
  2. AntiTbPdb: A database of anti-tubercular peptides.
  3. ApoCanD:  Database of Human Apoptotic Proteins in the context of cancer.
  4. B3Pdb: Archive of blood brain barrier-penetrating peptides
  5. BCIpep: Collection & compilation of B-cell epitopes from literature.
  6. BIAdb: A Database for Benzylisoquinoline Alkaloids.
  7. CancerDR: Cancer drug resistance database.
  8. CancerEnD: A database of cancer associated enhancers
  9. CancerLivER: A database of liver cancer gene expression resources and biomarkers.
  10. CancerPDF: Database of cancer-associated peptides of human bodyfluids.
  11. CancerPPD:  Database of anticancer peptides and proteins.
  12. Cancertope: A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer.
  13. CCDB: Database of genes involved in Cervix Cancer.
  14. ccPDB: Compilation and Creation of datasets from PDB.
  15. CPPsite: A web page for cell penetrating peptides.
  16. CPPsite 2.0:  A database of experimentally validated cell penetrating Peptides.
  17. csirdb:Identification of Cancer-specific siRNAs for personalized therapy.
  18. dbEM: A Database of Epigenetic Modifiers
  19. DenvInD: dengue virus inhibitors database for clinical and molecular research
  20. EbolaVCR: A web-based resource for designing therapeutics against Ebola Virus.
  21. ECDB: Endometrial cancer gene database.
  22. EGFRindb: A database of EGF(Epidermal Growth Factor) receptors  (anticaner database).
  23. FermFooDb: Database of bioactive peptides derived from fermented foods
  24. HaptenDB: A database of haptens, provide comprehensive information about the hapten molecule.
  25. HemolytiK: A repository of experimentally validated hemolytic and non-hemolytic peptides.
  26. HerceptinR: Information about assays performend to test sensitivity/resistance of Herceptin Antibodies.
  27. HIVbio: HIV related bioinformatics resources.
  28. HIVsir: A manually curated database of anti-HIV siRNAs.
  29. HMRbase: A manually curated database of hormones and their Receptors.
  30. HumCFS: A database of fragile sites in human chromosome.
  31. MHCBN: A database od Major Histocompatibility Complex (MHC) Binding,Non-binding peptides.
  32. MHCBN4: A database of MHC/TAP binding peptides and T-cell epitopes.
  33. MtbVeb: A webportal for designing vaccine against drug resistant and emerging strains of M. tuberculosis.
  34. NPACT: A curated database of plant derived natural compounds that exhibit anti-cancerous activity.
  35. OvirusTdb: Resource To Explore The Therapeutic Potential Of Oncolytic Viruses
  36. OXDbase: A database of Biodegradative oxygenase.
  37. ParaPep: Compilation of experimentally validated anti-parasitic peptides and their structures. 
  38. PCMdb: A database of methylated genes found in pancreatic cancer cell lines and tissues.
  39. PEPlife: Database of experimentally validated therapeutic peptides and their half lives.
  40. PolysacDB:  A comprehensive Database of microbial Polysaccharide antigens and their antibodies.
  41. PPDbench: Benchmarking of docking software on protein-peptide complexes
  42. ProCanBio: Database of manually curated biomarkers for Prostate Cancer
  43. PRRDB: A database of pattern recognition receptor.
  44. PRRDB 2.0: Database of pattern-recognition receptors and their ligands.
  45. RareLSD: Manually curated database of lysosomal enzymes associated with rare diseases
  46. SAPdb: A database of nanostructure formed by self assembly of short peptide.
  47. SATPdb: A database of structurally annotated therapeutic peptides .
  48. STARPDB: A webserver for annotating structure of a protein using simililarity based approach.
  49. THPdb: A database of FDA approved therapeutic peptides and proteins.
  50. TopicalPdb: A Database of Topically Administered Peptide.
  51. TumorHope: A comprehensive database of Tumor Homing Peptides.
  52. TumorHPD: A webserver for predicting and designing of tumor homing peptides.
  53. VLCvirus: Web Resource For Designing Subunit Vacccine Candidates Against Lung Cancer Associated Viruses
  54.  ZikaVR: An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and Therapeutic Analysis

Important Resources 

  1. ABsource: Antibody related resources 
  2. BioTherapi: Bioinformatics for Therapeutic Peptides and Proteins
  3. CanceRES: Cancer Informatics Portal 
  4. CRDD: Computational Resources for Drug Disovery
  5. CRIP: Computational Resources for molecular Interaction Prediction
  6. Drug: Drug Informatics @ Raghava's Group
  7. GDPbio: Genome based prediction of Diseases and Personal Medicine
  8. GenomeSRS: Genome Sort Read Sequences (SRS) related resources 
  9. HIVbio: HIV related bioinformatics resources

External Links to web servers developed/mainatined by other groups

This section provides URL/links to important websites developed and maintained by other researchers. It exclude servers by Raghava's group, which is given in above section. 

  1. 1-CMDb: A Curated Database of Genomic Variations of the One-Carbon Metabolism Pathway.
  2. 3PFDB+: improved search protocol and update for the identification of representatives of protein sequence domain families.
  3. 3PFDB: 3PFDB a database of best representative PSSM profiles (BRPs) of protein families generated using a novel data mining approach.
  4. Actinobase: Database on molecular diversity phylogeny and biocatalytic potential of salt tolerant alkaliphilic actinomycetes.
  5. AntiAngioPred: A Server for Prediction of Anti-Angiogenic Peptides.
  6. Antigen-Antibody Interaction Database (AgAbDb): a compendium of antigen:antibody interactions.
  7. APMicroDB: A microsatellite database of Acyrthosiphon pisum.
  8. APSLAP: an adaptive boosting technique for predicting subcellular localization of apoptosis protein.
  9. AVPdb: a database of experimentally validated antiviral peptides targeting medically important viruses.
  10. BioDB Extractor: Customized data extraction system for commonly used bioinformatics databases.
  11. bPE toolkit: Toolkit for computational protein engineering.
  12. BreCAN-DB: A repository cum browser of personalized DNA breakpoint profiles of cancer genomes.
  13. CAMP: a useful resource for research on antimicrobial peptides.
  14. CAMP: Collection of sequences and structures of antimicrobial peptides.
  15. ChloroMitoSSRDB 2.00: more genomes, more repeats, unifying SSRs search patterns and on-the-fly repeat detection
  16. CicArMiSatDB: the chickpea microsatellite database.
  17. Circ2Traits: a comprehensive database for circular RNA potentially associated with disease and traits.
  18. CKB: A Compendium of Cyanobacterial Genomes and Proteomes.
  19. ClassAMP: a prediction tool for classification of antimicrobial peptides.
  20. ClosIndb: A resource for computationally derived information from clostridial genomes.
  21. CMsDB: Development of genome-wide informative simple sequence repeat markers for large-scale genotyping applications in chickpea and development of web resource.
  22. Coffee Genome Hub: Transcripts of pectin-degrading enzymes and isolation of complete cDNA sequence of a pectate lyase gene induced by coffee white stem borer (Xylotrechus quadripes) in the bark tissue of Coffea canephora (robusta coffee)
  23. CPAD: A Repository of Manually Curated Experimental Data on Protein and Peptide Aggregation.
  24. CRCDA: Comprehensive resources for cancer NGS data analysis.
  25. CyanoPhyChe: a database for physico:chemical properties structure and biochemical pathway information of cyanobacterial proteins.
  26. DB Dehydrogenase: an online integrated structural database on enzyme dehydrogenase.
  27. dbDiarrhea: the database of pathogen proteins and vaccine antigens from diarrheal pathogens.
  28. DBETH: a Database of Bacterial Exotoxins for Human.
  29. dEMBF: A Comprehensive Database of Enzymes of Microalgal Biofuel Feedstock.
  30. DenHunt : A Comprehensive Database of the Intricate Network of Dengue-Human Interactions.
  31. DIACAN: Integrated Database for Antidiabetic and Anticancer Medicinal Plants.
  32. DOR: a Database of Olfactory Receptors Integrated Repository for Sequence and Secondary Structural Information of Olfactory Receptors in Selected Eukaryotic Genomes.
  33. DREMECELS: A Curated Database for Base Excision and Mismatch Repair Mechanisms Associated Human Malignancies.
  34. EssOilDB: a database of essential oils reflecting terpene composition and variability in the plant kingdom.
  35. FBIS: A regional DNA barcode archival & analysis system for Indian fishes.
  36. FiloBase: Essential proteins and possible therapeutic targets of Wolbachia endosymbiont and development of FiloBase--a comprehensive drug target database for Lymphatic filariasis.
  37. FmMDb: a versatile database of foxtail millet markers for millets and bioenergy grasses research.
  38. Haemophilus influenzae Genome Database (HIGDB): a single point web resource for Haemophilus influenzae.
  39. HDRNAS: An Automated Hierarchical Database of RNA Structures.
  40. HGEx-Erdb: Endometrial receptivity:
  41. HIPdb: a database of experimentally validated HIV inhibiting peptides.
  42. HNOCDB: a comprehensive database of genes and miRNAs relevant to head and neck and oral cancer.
  43. HPRD: Human Protein Reference Database:2009 update.
  44. HprotDB: The Halophile protein database.
  45. HPVdetector: NGS-based approach to determine the presence of HPV and their sites of integration in human cancer genome.
  46. HSPIR: a manually annotated heat shock protein information resource.
  47. Human Disease Insight: An integrated knowledge-based platform for disease-gene-drug information.
  48. Human Proteome Map: A draft map of the human proteome.
  49. HumanViCe: host ceRNA network in virus infected cells in human.
  50. HypoxiaDB: a database of hypoxia:regulated proteins.
  51. IGDD: Indian genetic disease database.
  52. IGVBrowser: a genomic variation resource from diverse Indian populations.
  53. Junker: an intergenic explorer for bacterial genomes.
  54. JUZBOX: a web server for extracting biomedical words from the protein sequence.
  55. KinG: a database of protein kinases in genomes.
  56. Lectindb: a plant lectin database.
  57. LenVarDB: database of length:variant protein domains.
  58. lnCeDB: database of human long noncoding RNA acting as competing endogenous RNA.
  59. LncRBase: an enriched resource for lncRNA information.
  60. LySDB : Lysozyme Structural DataBase.
  61. Manually curated database of rice proteins: a literature based manually curated protein centric database of rice proteins.
  62. MGExUdb: a mammalian uterus database for expression:based cataloguing of genes across conditions including endometriosis and cervical cancer.
  63. MICdb3.0: a comprehensive resource of microsatellite repeats from prokaryotic genomes
  64. MIPModDB: a central resource for the superfamily of major intrinsic proteins.
  65. miRnalyze: An interactive database linking tool to unlock intuitive microRNA regulation of cell signaling pathways.
  66. MitoSatPlant: mitochondrial microsatellites database of viridiplantae.
  67. MMNDB: Mammalian Mitochondrial ncRNA Database.
  68. MMpI: A WideRange of Available Compounds of Matrix Metalloproteinase Inhibitors.
  69. MPDB: Molecular Pathways Brain Database.
  70. MPGDB: Mycobacteriophage genome database.
  71. MTBPCDB: Mycobacterium tuberculosis proteome comparison database.
  72. MYCbase: A database of functional sites and biochemical properties of Myc in both normal and cancer cells.
  73. MycobacRV: Integrative immunoinformatics for Mycobacterial diseases in R platform.
  74. MycoProteaseDB: Useful resource for Mycobacterium tuberculosis complex and nontuberculous mycobacterial proteases.
  75. MycoRRdb: a database of computationally identified regulatory regions within intergenic sequences in mycobacterial genomes.
  76. MycoSec: A database for Mycobacterium secretome analysis:
  77. Myosinome: a database of myosins from select eukaryotic genomes to facilitate analysis of sequence:structure:function relationships.
  78. NALDB: Nucleic acid ligand database for small molecules targeting nucleic acid.
  79. NEIHPID: Knowledge Base for Helminth Parasites.
  80. NeuroDNet : an open source platform for constructing and analyzing neurodegenerative disease networks.
  81. NNvPDB: Neural Network based Protein Secondary Structure Prediction with PDB Validation.
  82. nonAUG: A survey of mRNA sequences with a non:AUG start codon in RefSeq database.
  83. novPTMenzy: a database for enzymes involved in novel post-translational modifications.
  84. Onco-Regulon: An integrated database and software suite for site specific targeting of transcription factors of cancer genes.
  85. OncomiRdbB: a comprehensive database of microRNAs and their targets in breast cancer.
  86. PALI: a database of Phylogeny and ALIgnment of homologous protein structures.
  87. Pancreatic Cancer Database: an integrative resource for pancreatic cancer.
  88. PASS2 version 4: an update to the database of structure:based sequence alignments of structural domain superfamilies.
  89. PASS2.5: Database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features.
  90. PASS2: an automated database of protein alignments organised as structural superfamilies.
  91. PCOSKB: A KnowledgeBase on genes diseases ontology terms and biochemical pathways associated with PolyCystic Ovary Syndrome.
  92. PDBparam: Online Resource for Computing Structural Parameters of Proteins.
  93. PfalDB: an integrated drug target and chemical database for Plasmodium falciparum.
  94. PIMADb: A Database of Protein-Protein Interactions in Huge Macromolecular Assemblies.
  95. PlantRGS: a web server for the identification of most suitable candidate reference genes for quantitative gene expression studies in plants.
  96. Plasma Proteome Database: a resource for proteomics research.
  97. PPDB: A Tool for Investigation of Plants Physiology Based on Gene Ontology.
  98. PrediQt-Cx: post treatment health related quality of life prediction model for cervical cancer patients.
  99. ProInflam: A webserver for the prediction of proinflammatory antigenicity of peptides and proteins.
  100. PromBase: a web resource for various genomic features and predicted promoters in prokaryotic genomes.
  101. PromBase: High quality annotation of promoter regions for 913 bacterial genomes.
  102. ProtVirDB: a database of protozoan virulent proteins.
  103. PpTFDB: A pigeonpea transcription factor database for exploring functional genomics in legumes.
  104. PvTFDB: A Phaseolus vulgaris transcription factors database for expediting functional genomics in legumes.
  105. QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice.
  106. RCDB: Renal Cancer Gene Database.
  107. RiceSRTFDB: a database of rice transcription factors containing comprehensive expression cis:regulatory element and mutant information to facilitate gene function analysis.
  108. RNABP COGEST: a resource for investigating functional RNAs.
  109. RV-Typer: A Web Server for Typing of Rhinoviruses Using Alignment-Free Approach.
  110. SeeHaBITaT: A server on bioinformatics applications for Tospoviruses and other species.
  111. SeriPort: A comprehensive view of the web-resources related to sericulture.
  112. SigMol: Repertoire of quorum sensing signaling molecules in prokaryotes.
  113. siRNAmod: A database of experimentally validated chemically modified siRNAs.
  114. SMBMDb: First whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications.
  115. SMS 2.0: an updated database to study the structural plasticity of short peptide fragments in non:redundant proteins.
  116. STIFDB2: an updated version of plant stress:responsive transcription factor database with additional stress signals stress:responsive transcription factor binding sites and stress:responsive genes in Arabidopsis and rice.
  117. Streptococcus pneumoniae Genome Database (SPGDB): a database for strain specific comparative analysis of Streptococcus pneumoniae genes and proteins.
  118. SUPFAM: a database of sequence superfamilies of protein domains.
  119. SUPFAM: implications for structural genomics and function annotation in genomes.
  120. SVMPBPred: SVM based protein block prediction method using sequence profiles and secondary structures.
  121. TaxKB: A knowledge base for new taxane-related drug discovery.
  122. Tbvar: A comprehensive genome variation resource for Mycobacterium tuberculosis.
  123. The Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail for zebrafish gene annotation.
  124. THGS: a web:based database of Transmembrane Helices in Genome Sequences.
  125. TMC-SNPdb:: An Indian germline variant database derived from whole exome sequences.
  126. Tomato genomic resources database: an integrated repository of useful tomato genomic information for basic and applied research.
  127. TRABAS: a database for transcription regulation by ABA signaling.
  128. TRIPATH: A Biological Genetic and Genomic Database of Three Economically Important Fungal Pathogen of Wheat :
  129. VIRmiRNA: a comprehensive resource for experimentally validated viral miRNAs and their targets.
  130. VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA.
  131. VPDB: Viral Protein Structural Database.
  132. WebGeSTer DB: a transcription terminator database.
  133. ZifBASE: a database of zinc finger proteins and associated resources.