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Resources (A-Z)

Complete list of computational resources from Raghava's Group

  1. Ab-Affi: Computer program for calculating affinity of a monoclonal antibody using non-competitive ELISA.
  2. ABCpred: Mapping of B-cell epitope(s) in an antigen sequence, using artificial neural network.
  3. ABCRpred: Prediction of antibiotic resistant strains of bacteria from their beta-lactamases protein
  4. ABMPred: Prediction of AntiBacterial Compounds against MurA Enzyme.
  5. ADPint: Predicion of ADP interacting residue.
  6. AHTpin: Designing and virtual screening of antihypertensive peptides.
  7. ALGpred: Prediction of allergenic proteins and mapping of IgE epitopes in antigens.
  8. AlgPred 2.0: An improved method for predicting allergenic proteins and mapping of IgE epitopes
  9. ALPHApred: A neural network based method for predicting alpha-turn in a protein.
  10. AntiAngiopred: A Server for Prediction of Anti-Angiogenic Peptides.
  11. AntiBP: Mapping of antibacterial peptides in a protein sequence.
  12. AntiBP2: Mapping of antibacterial peptides in a protein sequence.
  13. AntiCP: Prediction and design of anticancer peptides.
  14. AntiCP 2.0: An updated model for predicting anticancer peptides.
  15. AntiFP: A Prediction server for Antifungal Peptide.
  16. Antifp: Prediction of Antifungal Peptides
  17. AntigenDB: An immunoinformatics database of pathogen antigens.
  18. AntiMPmod: Predicts the antimicrobial property of the chemically modified peptide.
  19. AntiTbPdb: A database of anti-tubercular peptides.
  20. AntiTbPdb: knowledgebase of anti-tubercular peptides.
  21. AntiTbPred: Prediction of antitubercular peptides.
  22. ApoCanD: Database of Human Apoptotic Proteins in the context of cancer.
  23. APSSP: Advanced Protein Secondary Structure Prediction Server.
  24. APSSP2: Prediction of secondary structure of proteins from their amino acid sequence.
  25. Ar_NHpred: Identification of aromatic-backbone NH interaction in protein residues.
  26. ATPint: Identification of ATP binding sites in ATP-binding proteins.
  27. B3Pdb: Archive of blood-brain barrier-penetrating peptides
  28. B3Pred: Prediction of Blood-Brain Barrier penetrating peptides
  29. BCEpred: Prediction of linear B-cell epitopes, using Physico-chemical properties.
  30. BCIpep: Collection & compilation of B-cell epitopes from literature.
  31. BetaTPred: Statistical-based method for predicting Beta Turns in a protein.
  32. BetaTPred2: Statistical-based method for predicting Beta Turns in a protein.
  33. BetaTPred3: Prediction of beta turns and their types.
  34. BetaTurns: Prediction of beta turn types.
  35. BhairPred: Prediction of beta hairpins in proteins using ANN and SVM techniques.
  36. BIAdb: A Database for Benzylisoquinoline Alkaloids.
  37. BioTherapi: Bioinformatics for Therapeutic Peptides and Proteins.
  38. BTEVAL: Evaluation of beta-turns prediction methods.
  39. BTXpred: A server for predicting bacterial toxins.
  40. CancerCSP: Gene expression-based biomarkers for discriminating early and late stage of clear cell renal cancer.
  41. CancerCSP: To predict stage of ccRCC using gene expression data derived from RNAseq experiments.
  42. CancerDP: Prioritization of anticancer drugs against a cancer using genomic features of cancer cells.
  43. CancerDR: Cancer drug resistance database.
  44. CancerEnD: A database of cancer associated enhancers
  45. CanceRES: Cancer Informatics Portal.
  46. CancerIN: A web server for predicting anticancer activity of molecules.
  47. CancerLivER: A database of liver cancer gene expression resources and biomarkers.
  48. CancerLSP: Web-bench Liver cancer stage prediction Server.
  49. CancerPDF:  Database of cancer-associated peptides of human bodyfluids.
  50. CancerPDF: Repository of cancer-associated peptidome found in human biofluids
  51. CancerPPD:   Database of anticancer peptides and proteins.
  52. CancerPred:  Prediction of the cancerlectins.
  53. CancerSPP: Web server to predict the progression of skin cancer.
  54. Cancertope:  A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer.
  55. CancerUBM:  Web bench for analysis of proteomics data and prediction of cancer status of a urine samples.
  56. CBTOPE:  Conformational B-cell Epitope prediction.
  57. CCDB:  Database of genes involved in Cervix Cancer.
  58. ccPDB:  Compilation and Creation of datasets from PDB.
  59. ccPDB 2.0: An updated version of datasets created and compiled from Protein Data Bank.
  60. CellPPD:  Computer-aided Designing of efficient cell penetrating peptides.
  61. CellPPDMod: Predicting the cell-penetrating property of modified peptides.
  62. ChAlPred: Webserver for predicting chemical allergens
  63. ChemoPred:  A server to predict chemokines and their receptor
  64. CHpredicts:  Prediction of CH-O, CH-PI interactions in backbone residues of a protein 
  65. Cmcrpred: Risk prediction in cutaneous melanoma (CM) patients using clinical features
  66. COPid:  Composition based identification and classification of proteins.
  67. CoronaVIR: Developed to maintain the predicted and existing information on SARS-CoV-2.
  68. CPPsite:  A web page for cell penetrating peptides.
  69. CPPsite 2.0:   A database of experimentally validated cell penetrating Peptides.
  70. CRCRpred: Used to distinguish high risk CRC patients from low risk CRC patients given the protein concentration of one or more apoptotic proteins.
  71. CRDD:  Computational resources for drug discovery.
  72. CRIP:  Computational Resources for molecular Interaction Prediction
  73. CTLPred:  A direct method for prediction of CTL epitopes. 
  74. CyclinPred:  CyclinPred is a SVM based prediction method to identify novel cyclins.
  75. CytoPred:  It is a webserver for prediction and classification of cytokines.
  76. DADpred:  Prediction of drugs against aspartate semialdehyde dehydrogenase of DAP pathway.
  77. DAMpro:  Disease Associated Mutations in Proteins.
  78. dbEM:  A Database of Epigenetic Modifiers
  79. DenvInD: dengue virus inhibitors database for clinical and molecular research
  80. desiRam:  Designing of highly efficient siRNA with minimum mutation approach
  81. DiPCell:  Designing of inhibitors against pancreatic cancer cell lines.
  82. DNAbinder:  A webserver for predicting DNA-binding proteins.
  83. DNAint:  Prediction of DNA Interacting Residues.
  84. DNAOPT:  Computer program for optimizing the conditions of gel electrophoresis and SDS-PAGE.
  85. DNASIZE:  Computer program for computing the size of DNA fragments from gel data using a graphical method.
  86. DPROT: SVM-based method for predicting of disordered proteins.
  87. DrugMint:  A web server for identification of drug like molecules.
  88. EbolaVCR:  A web-based resource for designing therapeutics against Ebola Virus.
  89. ECDB:  Endometrial cancer gene database.
  90. ECGPred:  Analsis of expresion data and correlation between gene expression and nucleotides composition of genes.
  91. EGFRindb:  A database of EGF(Epidermal Growth Factor) receptors  (anticaner database).
  92. EGFRpred:  A web service for the predicting and designing of inhibitors against EGFR (anticancer drugs).
  93. EGPred:  Prediction of gene (protein coding regions) in eukaryote genomes that includes introns/exons.
  94. ELISAeq:  Computer program for determining the concentration of antibody/antigen from ELISA data.
  95. ESLpred:  Subcellular localization of the eukaryotic proteins using dipeptide compostion and PSI-BLAST.
  96. ESLpred2:  Advanced method for subcellular localization of eukaryotic proteins.
  97. FADpred :  A webserver for the prediction of FAD interacting residues.
  98. FermFooDb: Database of bioactive peptides derived from fermented foods
  99. fisipred:  Phi-Psi angle prediction using average angle prediction technique.
  100. FTG:  Locating probable protein coding region in nucleotide sequence using FFT based algorithm.
  101. GammaPred:  Identification of gamma-turn containing residues in a given protein sequence.
  102. GDoQ:  Prediction of GLMU inhibitors (anti-tubeculosis inhibitors) using QSAR and docking apprach.
  103. GDPbio:  Genome based prediction of Diseases and Personal Medicine
  104. GlycoEP:  Prediction of C-, N- and O-glycosylation site in eukaryotic proteins. 
  105. GlycoPP:  Prediction of potential N-and O-glycosites in prokaryotic proteins.
  106. GMAP:  Computer program for mapping potential restriction endonuclease sites in non-ambiguous DNA. 
  107. GMPEsi:  Generalized Model for Predicting Efficacy of siRNAs.
  108. GPCRpred:  Prediction of families and superfamilies of G-protein coupled receptors (GPCR).
  109. GPCRsclass:  This webserver predicts amine type of G-protein coupled receptors
  110. GPSR:  A resource for genomocs, proteomics and system biology
  111. GSTpred:  SVM-based method for predicting Glutathione S-transferase protein.
  112. GTPbinder:  Identification of GTP binding residue in protein sequences. 
  113. HaptenDB:  A database of haptens, provide comprehensive information about the hapten molecule.
  114. HCCpred: A webserver to predict Hepatocellular carcinoma (HCC).
  115. HemolytiK:  A repository of experimentally validated hemolytic and non-hemolytic peptides.
  116. HemoPI:  Prediction and virtual screening of hemolytic peptides.
  117. HemoPImod: A Method for Predicting Hemolytic Potency of Chemically Modified Peptides From Its Structure.
  118. HerceptinR:  Information about assays performend to test sensitivity/resistance of Herceptin Antibodies.
  119. HIVbio:  HIV related bioinformatics resources.
  120. HIVcoPRED:  Predicting coreceptor used by HIV-1 from Its V3 loop amino acid sequence.
  121. HIVfin:  Prediction of Fusion Inhibitors against HIV (drugs against HIV)
  122. HIVint:  Prediction of protein-protein interaction between HIV and Human proteins.
  123. HLA-DR4Pred:  Identification of HLA-DRB1*0401(MHC class II alleles) binding peptides.
  124. HLP:  Designing of stable antibacterial peptides.
  125. HMRbase:  A manually curated database of hormones and their Receptors.
  126. HSLpred:  Prediction of subcellular localization of human proteins with high accuracy
  127. HumCFS:  A database of fragile sites in human chromosome.
  128. HumCFS: Database of fragile sites in human chromosomes
  129. icaars:  Identification & Classification of Aminoacyl tRNA Synthetases.
  130. IFNepitope:  A server for predicting and designing interferon-gamma inducing epitopes.
  131. IgPred:  Prediction of antibody specific B-cell epitope.
  132. IL-10pred: For designing IL-10 inducing peptides.
  133. IL-6Pred: Predition of interleukin -6 inducing peptides.
  134. IL10pred:  Prediction of Interleukin-10 inducing peptides.
  135. IL2Pred: Prediction of IL-2 inducing peptides in humans
  136. IL4IFNG:  Computer program for computing of murine interleukin-4 and interferon-gamma. 
  137. IL4pred:  In silico platform for designing and disovering of Interleukin-4 inducing peptides.
  138. imRNA:  Prediction of Immunomodulatory RNAs.
  139. imRNA: For designing RNA-based therapeutics and vaccine adjuvants.
  140. KiDoQ:  Prediction of inhibition against dihydrodipicolinate synthase of M. Tuberculosis.
  141. LBtope:  A server for predicting linear B-cell epitopes.
  142. LGEpred:  Correlation analysis and prediction of genes expression from amino acid sequence of proteins.
  143. LPIcom:  Analysis and prediction of ligand protein interaction.
  144. MARSpred:  Prediction of mitochondrial aminoacyl tRNA synthetases.
  145. MDRIpred:  Predicting inhibitor against drug tolrent M.Tuberculosis.
  146. MetaPred:  Prediction of Cytochrome P450 Isoform responsible for metabolizing a drug molecule.
  147. MHCBN:  A database of Major Histocompatibility Complex (MHC) Binding, Non-binding peptides .
  148. MHCBN:  A database od Major Histocompatibility Complex (MHC) Binding,Non-binding peptides.
  149. MHCBN4:  A database of MHC/TAP binding peptides and T-cell epitopes.
  150. MitPred:  Prediction of mitochondrial proteins using SVM and hidden Markov model.
  151. MtbVeb:  A webportal for designing vaccine against drug resistant and emerging strains of M. tuberculosis.
  152. NADbinder:  Prediction of NAD interacting residues in proteins.
  153. NAGbinder: An approach for identifying N-acetylglucosamine interacting residues of a protein from its primary sequence
  154. NeuroPIpred: A tool to predict, design and scan insect neuropeptides.
  155. nHLAPred:  A neural network based method for predicting MHC Class-I binders.
  156. NPACT:  A curated database of plant derived natural compounds that exhibit anti-cancerous activity.
  157. NPpred:   A webserver for the prediction of nuclear proteins.
  158. NRpred:   A SVM based method for the classification of nuclear receptors .
  159. ntEGFR:  QSAR-Based Models for designing inhibitors against Wild and Mutant EGFR (anti-cancer drug).
  160. NTXpred:  Identification of neurotoxins their source and function from primary amino acid sequence.
  161. OSCADD:  Open Source for Computer-Aided Drug Discovery portal is for chemoinformatics and pharmacoinformatics.
  162. OSDDlinux:  A customize operating system for drug discovery.
  163. OvirusTdb: Resource To Explore The Therapeutic Potential Of Oncolytic Viruses
  164. OXDbase:  A database of Biodegradative oxygenase.
  165. OXYpred:  Classification and prediction of oxygen binding proteins.
  166. PAAINT:  A webservice for predicting residue-residue contacts in proteins.
  167. ParaPep:  Compilation of experimentally validated anti-parasitic peptides and their structures. 
  168. Pcleavage:  Identification of protesosomal cleavage sites in a protein sequence. 
  169. PCMdb:  A database of methylated genes found in pancreatic cancer cell lines and tissues.
  170. PEPlife:  Database of experimentally validated therapeutic peptides and their half lives.
  171. PEPstr:  Prediction of structure of peptides.
  172. PEPstrMOD:  Structural prediction of peptides containing natural, non-natural and modified residues.  
  173. PFMpred:  Predicting mitochondrial proteins of malaria parasite Plasmodium falciparum.
  174. PHDcleav:  Prediction of human Dicer cleavage sites using sequence and secondary structure of miRNA precursors. 
  175. PLDbench:  Benchmarking of docking software on peptide-ligand complexes. 
  176. PlifePred:  An insilico method to design and predict the half life of modified and natural peptides in blood. 
  177. PlifePred: Predicting the half-life of natural and modified peptides in blood.
  178. PolyApred:  Prediction of polyadenylation signal (PAS) in human DNA sequence.
  179. PolysacDB:   A comprehensive Database of microbial Polysaccharide antigens and their antibodies.
  180. PPDBench:   Benchmarking of docking software on protein-peptide complexes.
  181. Pprint:   A  web-server for predicting RNA-binding residues of a protein.
  182. PreMieR:   A webserver for the prediction of Mannose Interacting residue.
  183. ProCanBio: Database of manually curated biomarkers for Prostate Cancer
  184. ProCarDB:  A database of bacterial carotenoids.
  185. PROGLYCPROT:  Database of experimentally characterized eubacterial and archaeal glycoproteins.
  186. ProPred:  A webserver to  predict MHC Class-II binding regions in an antigen sequence.
  187. ProPred-1:  Prediction of  promiscuous MHC Class-I binders.
  188. ProPrInt:  A web-server predicts physical or functional interactions between protein molecules.
  189. PRRDB:  A database of pattern recognition receptor.
  190. PRRDB 2.0: Database of pattern-recognition receptors and their ligands.
  191. PRRpred: Prediction of pattern recognition receptors
  192. PSAWeb:  Analysis of Protein Sequence and Multiple Alignment.
  193. PSEApred:  Prediction of Plasmodium Secretory and Infected Erythrocyte Associated Proteins.
  194. PSLpred:  Predict subcellular localization of prokaryotic proteins.
  195. QASpro:  A webserver for the Quality Assesment of Protein Structure.
  196. RareLSD: Manually curated database of lysosomal enzymes associated with rare diseases
  197. RNAcon:  A web-server for the prediction and classification of non-coding RNAs.
  198. RNAint:  Identification of RNA interacting residues in a protein.
  199. RNApin:  Prediction of Protein Interacting Nucleotides (PINs) in RNA sequences.
  200. RNApred:  A webserver for the prediction of RNA binding proteins.
  201. RRCpred:  A Webserver for predicting residue-residue contact.
  202. RSLpred:  A method for the subcellular localization prediction of rice proteins.
  203. SAMbinder: Web Server for Predicting S-Adenosyl-L-Methionine Binding Residues of a Protein From Its Amino Acid Sequence
  204. SAPdb:  A database of nanostructure formed by self assembly of short peptide.
  205. SAPdb: Database of short peptides and the corresponding nanostructures formed by self-assembly
  206. SARpred:  A neural network based method predicts the real value of surface acessibility.
  207. SATPdb:  A database of structurally annotated therapeutic peptides .
  208. Sigma70Pred: A highly accurate method for predicting sigma70 promoter in prokaryotic genome
  209. siRNApred:  SVM based method for predicting efficacy value of siRNA.
  210. SKCMhrp: For predicting the risk status in cutaneous melanoma patients
  211. SRF:  A program to find repeats through an analysis of the power spectrum of a given DNA sequence. 
  212. SRTpred:  A method for the classification of protein sequence as secretory or non-secretory protein.
  213. STARPDB:  A webserver for annotating structure of a protein using simililarity based approach.
  214. STAT3In: Prediction of inhibitors against STAT3
  215. TAPPred:  A webserver for predicting binding affinity of peptides toward the TAP transporter.
  216. TBBpred:  A webserver for the prediction of transmembrane Beta barrel regions in a given protein sequence.
  217. TBpred:  A webserver  that predicts four subcellular localization of mycobacterial proteins.
  218. THPdb:  A database of FDA approved therapeutic peptides and proteins.
  219. THPdb: Database of FDA-approved peptide and protein therapeutics.
  220. TmhcPred:  A webserver that predict MHC Class I and II binding peptides.
  221. TopicalPdb:  A Database of Topically Administered Peptide.
  222. TopicalPdb: Database of topically delivered peptides
  223. ToxinPred:  An in silico method, which is developed to predict and design toxic/non-toxic peptides.
  224. ToxiPred:  A server for prediction of aqueous toxicity of small chemical molecules in T. pyriformis.
  225. tRNAmod:  The tRNAmod is a web-server for the prediction of transfer RNA (tRNA) modifications.
  226. TSP-PRED:  A webservice for predicting Tertiary Structure of proteins.
  227. TumorHope:  A comprehensive database of Tumor Homing Peptides.
  228. TumorHPD:  A webserver for predicting and designing of tumor homing peptides.
  229. VaccineDA:  A webserver for prediction of oligodeoxynucleotide vaccine adjuvant.
  230. VacTarBac: Proteomic based vaccine design for pathogenic bacteria.
  231. VaxinPAD:  A webserver for designing peptide based vaccine adjuvant.
  232. VaxinPAD: Predict and design immunomodulatory peptides or A-cell epitopes
  233. VGIchan:  Voltage gated ion channel prediction server.
  234. VICMPpred:   Prediction of Virulence factors, Information molecule, Cellular process and Metabolism molecule in the Bacterial proteins.
  235. VitaPred:  A webserver for predicting the vitamin interacting residue.
  236. VLCvirus: Web Resource For Designing Subunit Vacccine Candidates Against Lung Cancer Associated Viruses
  237. XIAPin:  Designing of efficient inhibitors against apoptosis protein XIAP (inhibitor against drug resistance cancer).
  238. ZikaVR:  An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and Therapeutic Analysis

External Links to web servers developed/maintained 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. 16S classifier: a tool for fast and accurate taxonomic classification of 16S rRNA hypervariable regions in metagenomic datasets.
  3. 3D-NuS: A Web Server for Automated Modeling and Visualization of non-canonical 3-Dimensional Nucleic Acid Structures.
  4. 3DSDSCAR: Molecular dynamics simulation and quantum mechanical calculations on α:D:N:acetylneuraminic acid.
  5. 3DSDSCAR: a three dimensional structural database for sialic acid:containing carbohydrates through molecular dynamics simulation.
  6. 3dswappred: prediction of 3D domain swapping from protein sequence using Random Forest approach.
  7. 3PFDB: 3PFDB a database of best representative PSSM profiles (BRPs) of protein families generated using a novel data mining approach.
  8. 3PFDB+: improved search protocol and update for the identification of representatives of protein sequence domain families.
  9. AADS: an automated active site identification, docking, and scoring protocol for protein targets based on physicochemical descriptors.
  10. ABS-Scan: In silico alanine scanning mutagenesis for binding site residues in protein:ligand complex.
  11. Actinobase: Database on molecular diversity, phylogeny and biocatalytic potential of salt tolerant alkaliphilic actinomycetes.
  12. ANGDelMut : a web-based tool for predicting and analyzing functional loss mechanisms of amyotrophic lateral sclerosis:associated angiogenin mutations.
  13. AntiAngioPred: A Server for Prediction of Anti-Angiogenic Peptides.
  14. Antigen-Antibody Interaction Database (AgAbDb): a compendium of antigen:antibody interactions.
  15. AntiInflam: Prediction of anti-inflammatory proteins/peptides: an insilico approach.
  16. APA: A gene expression dataset analysis tool for identification and prioritization of differentially regulated and network rewired pathways.
  17. APMicroDB: A microsatellite database of Acyrthosiphon pisum.
  18. APPLE: Importance of functional groups in predicting the activity of small molecule inhibitors for Bcl-2 and Bcl-xL.
  19. APSLAP: an adaptive boosting technique for predicting subcellular localization of apoptosis protein.
  20. ARC: automated resource classifier for agglomerative functional classification of prokaryotic proteins using annotation texts.
  21. AtREA: Arabidopsis thaliana regulatory element analyzer.
  22. AVCpred: An integrated web server for prediction and design of antiviral compounds.
  23. AVP-IC50Pred: Multiple machine learning techniques-based prediction of peptide antiviral activity in terms of half maximal inhibitory concentration (IC50).
  24. AVPdb: a database of experimentally validated antiviral peptides targeting medically important viruses.
  25. AVPpred: collection and prediction of highly effective antiviral peptides.
  26. Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins.
  27. Bhageerath-H Strgen: A homology/ab initio hybrid algorithm for sampling near:native protein conformations.
  28. BioDB Extractor: Customized data extraction system for commonly used bioinformatics databases.
  29. BIOFIN: Prediction of Biofilm Inhibiting Peptides: An In silico Approach.
  30. Bisgoat: Locus minimization in breed prediction using artificial neural network approach.
  31. bPE toolkit: Toolkit for computational protein engineering.
  32. BreCAN-DB: A repository cum browser of personalized DNA breakpoint profiles of cancer genomes.
  33. CADB3.0: Conformational Angles DataBase
  34. CAMP: Collection of sequences and structures of antimicrobial peptides.
  35. CAMP: a useful resource for research on antimicrobial peptides.
  36. CAPi: Computational Model for Apicoplast Inhibitors Prediction Against Plasmodium Parasite.
  37. CARDIO-PRED: an in silico tool for predicting cardiovascular-disorder associated proteins.
  38. CDKIpred: Machine learning methods for prediction of CDK:inhibitors.
  39. CEMID: Mining of expressed sequence tag libraries of cacao for microsatellite markers using five computational tools.
  40. CEP: a conformational epitope prediction server.
  41. ChloroMitoSSRDB 2.00: more genomes, more repeats, unifying SSRs search patterns and on-the-fly repeat detection
  42. CicArMiSatDB: the chickpea microsatellite database.
  43. Circ2Traits: a comprehensive database for circular RNA potentially associated with disease and traits.
  44. CKB: A Compendium of Cyanobacterial Genomes and Proteomes.
  45. CLAP: a web:server for automatic classification of proteins with special reference to multi:domain proteins.
  46. ClassAMP: a prediction tool for classification of antimicrobial peptides.
  47. ClosIndb: A resource for computationally derived information from clostridial genomes.
  48. CmMDb: a versatile database for Cucumis melo microsatellite markers and other horticulture crop research.
  49. CMsDB: Development of genome-wide informative simple sequence repeat markers for large-scale genotyping applications in chickpea and development of web resource.
  50. 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)
  51. COILCHECK: an interactive server for the analysis of interface regions in coiled coils.
  52. COILCHECK+: Structural attributes for the recognition of weak and anomalous regions in coiled:coils of myosins and other motor proteins.
  53. CPAD: A Repository of Manually Curated Experimental Data on Protein and Peptide Aggregation.
  54. CRCDA: Comprehensive resources for cancer NGS data analysis.
  55. CREMOFAC: a database of chromatin remodeling factors.
  56. CSIdesigner: An siRNA designing tool with a unique functional off:target filtering approach.
  57. CTDB: An Integrated Chickpea Transcriptome Database for Functional and Applied Genomics.
  58. CyanoPhyChe: a database for physico:chemical properties, structure and biochemical pathway information of cyanobacterial proteins.
  59. CyanoPhyChe: a database for physico:chemical properties, structure and biochemical pathway information of cyanobacterial proteins.
  60. D-MATRIX: a web tool for constructing weight matrix of conserved DNA motifs.
  61. D2N: Distance to the native.
  62. DB Dehydrogenase: an online integrated structural database on enzyme dehydrogenase.
  63. dbDiarrhea: the database of pathogen proteins and vaccine antigens from diarrheal pathogens.
  64. DBETH: a Database of Bacterial Exotoxins for Human.
  65. dEMBF: A Comprehensive Database of Enzymes of Microalgal Biofuel Feedstock.
  66. DenHunt : A Comprehensive Database of the Intricate Network of Dengue-Human Interactions.
  67. DIACAN: Integrated Database for Antidiabetic and Anticancer Medicinal Plants.
  68. DIAL: a web:based server for the automatic identification of structural domains in proteins.
  69. DIM-Pred: Prediction of protein disorder on amino acid substitutions.
  70. DIRProt: A computational approach for discriminating insecticide resistant proteins from non-resistant proteins.
  71. Distributed chemical computing using ChemStar: an open source java remote method invocation architecture applied to large scale molecular data from PubChem.
  72. DOCKSCORE: a webserver for ranking protein-protein docked poses.
  73. DockYard: a repository to assist modeling of protein:protein docking.
  74. DOR: a Database of Olfactory Receptors, Integrated Repository for Sequence and Secondary Structural Information of Olfactory Receptors in Selected Eukaryotic Genomes.
  75. DREMECELS: A Curated Database for Base Excision and Mismatch Repair Mechanisms Associated Human Malignancies.
  76. DRGAS: a database of functional genetic variants and their phosphorylation states in human DNA repair systems.
  77. ECMIS: computational approach for the identification of hotspots at protein:protein interfaces.
  78. EnPPIpred: Prediction of Intra-Species Protein-Protein Interactions in Enteropathogens Facilitating Systems Biology Study.
  79. EssOilDB: a database of essential oils reflecting terpene composition and variability in the plant kingdom.
  80. ExSer: A standalone tool to mine protein data bank (PDB) for secondary structural elements.
  81. FaaPred: a SVM based prediction method for fungal adhesins and adhesin:like proteins.
  82. FAIR: A server for internal sequence repeats.
  83. FBIS: A regional DNA barcode archival & analysis system for Indian fishes.
  84. FBIS: A regional DNA barcode archival & analysis system for Indian fishes.
  85. FiloBase: Essential proteins and possible therapeutic targets of Wolbachia endosymbiont and development of FiloBase--a comprehensive drug target database for Lymphatic filariasis.
  86. FISH KARYOME: A chromosome database of fishes and other aquatic organisms.
  87. FishAMP: Development of Antimicrobial Peptide Prediction Tool for Aquaculture Industries.
  88. FMALIGN: Improvement of alignment accuracy utilizing sequentially conserved motifs.
  89. FMIMS: Identifying relevant group of miRNAs in cancer using fuzzy mutual information.
  90. FmMDb: a versatile database of foxtail millet markers for millets and bioenergy grasses research.
  91. FmTFDb: a foxtail millet transcription factors database for expediting functional genomics in millets.
  92. Folding RaCe: A robust method for predicting changes in protein folding rates upon point mutations.
  93. Fragment Finder: a web based software to identify similar three:dimensional structural motif.
  94. GAP: towards almost 100 percent prediction for β:strand:mediated aggregating peptides with distinct morphologies.
  95. ge-CRISPR : An integrated pipeline for the prediction and analysis of sgRNAs genome editing efficiency for CRISPR/Cas system.
  96. GEDAS: Gene Expression Data Analysis Suite.
  97. GingerRest: Computer aided gene mining for gingerol biosynthesis.
  98. GraProStr: Ranking the quality of protein structure models using sidechain based network properties.
  99. GREAM: A Web Server to Short-List Potentially Important Genomic Repeat Elements Based on Over-/Under-Representation in Specific Chromosomal Locations, Such as the Gene Neighborhoods, within or across 17 Mammalian Species.
  100. Haemophilus influenzae Genome Database (HIGDB): a single point web resource for Haemophilus influenzae.
  101. Hansa: an automated method for discriminating disease and neutral human nsSNPs.
  102. HARMONY: a server for the assessment of protein structures.
  103. HDRNAS: An Automated Hierarchical Database of RNA Structures.
  104. HGEx-Erdb: Endometrial receptivity:
  105. HGV&TB: a comprehensive online resource on human genes and genetic variants associated with tuberculosis.
  106. HIPdb: a database of experimentally validated HIV inhibiting peptides.
  107. HLaffy: Estimating peptide affinities for Class-1 HLA molecules by learning position-specific pair potentials.
  108. HNOCDB: a comprehensive database of genes and miRNAs relevant to head and neck and oral cancer.
  109. HORI: a web server to compute Higher Order Residue Interactions in protein structures.
  110. HPRD: Human Protein Reference Database:2009 update.
  111. HprotDB: The Halophile protein database.
  112. HPVbase: A knowledgebase of viral integrations, methylation patterns and microRNAs aberrant expression: As potential biomarkers for Human papillomaviruses mediated carcinomas.
  113. HPVdetector: NGS-based approach to determine the presence of HPV and their sites of integration in human cancer genome.
  114. HSPIR: a manually annotated heat shock protein information resource.
  115. HSplice: Identification of donor splice sites using support vector machine: a computational approach based on positional, compositional and dependency features.
  116. Hu-Vir: Molecular principles of human virus protein-protein interactions.
  117. Human Disease Insight: An integrated knowledge-based platform for disease-gene-drug information.
  118. Human Proteome Map: A draft map of the human proteome.
  119. HumanViCe: host ceRNA network in virus infected cells in human.
  120. HyPe: Prediction of peptidoglycan hydrolases- a new class of antibacterial proteins.
  121. HypoxiaDB: a database of hypoxia:regulated proteins.
  122. iAMPpred: Predicting antimicrobial peptides with improved accuracy by incorporating the compositional, physico-chemical and structural features into Chous general PseAAC.
  123. iCR: a web tool to identify conserved targets of a regulatory protein across the multiple related prokaryotic species.
  124. IGDD: Indian genetic disease database.
  125. IGIPT : Integrated genomic island prediction tool.
  126. IGVBrowser: a genomic variation resource from diverse Indian populations.
  127. IMEx: Imperfect Microsatellite Extractor.
  128. Intercalate: A DNA intercalation methodology for an efficient prediction of ligand binding pose and energetics.
  129. iRDP: Engineering Proteins for Thermostability with iRDP Web Server.
  130. IRESPred: Web Server for Prediction of Cellular and Viral Internal Ribosome Entry Site (IRES)
  131. IWS: integrated web server for protein sequence and structure analysis.
  132. Junker: an intergenic explorer for bacterial genomes.
  133. JUZBOX: a web server for extracting biomedical words from the protein sequence.
  134. KERA: A novel sequence and context based method for promoter recognition.
  135. KinG: a database of protein kinases in genomes.
  136. Layers: A molecular surface peeling algorithm and its applications to analyze protein structures.
  137. Lectindb: a plant lectin database.
  138. LenVarDB: database of length:variant protein domains.
  139. lnCeDB: database of human long noncoding RNA acting as competing endogenous RNA.
  140. LncRBase: an enriched resource for lncRNA information.
  141. LRRsearch: An asynchronous server:based application for the prediction of leucine:rich repeat motifs and an integrative database of NOD:like receptors.
  142. LySDB : Lysozyme Structural DataBase.
  143. M3db: Gene Network Rewiring to Study Melanoma Stage Progression and Elements Essential for Driving Melanoma.
  144. MaLDoSS: Prediction of donor splice sites using random forest with a new sequence encoding approach.
  145. Manually curated database of rice proteins: a literature based manually curated protein centric database of rice proteins.
  146. matK-QR classifier: A patterns based approach for plant species identification.
  147. MaxMod: a hidden Markov model based novel interface to MODELLER for improved prediction of protein 3D models.
  148. MeTA studio: a cross platform, programmable IDE for computational chemist.
  149. MGEx-Tdb: A novel tissue specific meta:analysis approach for gene expression predictions, initiated with a mammalian gene expression testis database.
  150. MGExUdb: a mammalian uterus database for expression:based cataloguing of genes across conditions, including endometriosis and cervical cancer.
  151. MGExUdb: a mammalian uterus database for expression:based cataloguing of genes across conditions, including endometriosis and cervical cancer.
  152. MICdb3.0: a comprehensive resource of microsatellite repeats from prokaryotic genomes
  153. MIPModDB: a central resource for the superfamily of major intrinsic proteins.
  154. miRMOD: A tool for identification and analysis of 5 and 3 miRNA modifications in Next Generation Sequencing small RNA data.
  155. miRnalyze: An interactive database linking tool to unlock intuitive microRNA regulation of cell signaling pathways.
  156. MirtronPred: Identification of mirtrons in rice using MirtronPred: a tool for predicting plant mirtrons.
  157. MitoSatPlant: mitochondrial microsatellites database of viridiplantae.
  158. MMNDB: Mammalian Mitochondrial ncRNA Database.
  159. MMpI: A WideRange of Available Compounds of Matrix Metalloproteinase Inhibitors.
  160. modPDZpep: A web resource for structure based analysis of human PDZ-mediated interaction networks.
  161. MOGA-SVM: Combining Pareto:optimal clusters using supervised learning for identifying co:expressed genes.
  162. MP3: a software tool for the prediction of pathogenic proteins in genomic and metagenomic data.
  163. MPDB: Molecular Pathways Brain Database.
  164. MPGDB: Mycobacteriophage genome database.
  165. MTBPCDB: Mycobacterium tuberculosis proteome comparison database.
  166. MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease.
  167. MYCbase: A database of functional sites and biochemical properties of Myc in both normal and cancer cells.
  168. MycobacRV: Integrative immunoinformatics for Mycobacterial diseases in R platform.
  169. Mycobacterium tuberculosis Structural proteome.: Structural annotation of Mycobacterium tuberculosis proteome.
  170. MycoProteaseDB: Useful resource for Mycobacterium tuberculosis complex and nontuberculous mycobacterial proteases.
  171. MycoRRdb: a database of computationally identified regulatory regions within intergenic sequences in mycobacterial genomes.
  172. MycoRRdb: a database of computationally identified regulatory regions within intergenic sequences in mycobacterial genomes.
  173. MycoSec: A database for Mycobacterium secretome analysis:
  174. Myosinome: a database of myosins from select eukaryotic genomes to facilitate analysis of sequence:structure:function relationships.
  175. NALDB: Nucleic acid ligand database for small molecules targeting nucleic acid.
  176. NAPS: Network Analysis of Protein Structures.
  177. NEIHPID: Knowledge Base for Helminth Parasites.
  178. NetSlim: High confidence curated signaling maps.
  179. NeuroDNet : an open source platform for constructing and analyzing neurodegenerative disease networks.
  180. NEXCADE: perturbation analysis for complex networks.
  181. NEXCADE: perturbation analysis for complex networks.
  182. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data.
  183. NIP-NSc: New measures for estimating surface complementarity and packing at protein:protein interfaces.
  184. NNvPDB: Neural Network based Protein Secondary Structure Prediction with PDB Validation.
  185. nonAUG: A survey of mRNA sequences with a non:AUG start codon in RefSeq database.
  186. novPTMenzy: a database for enzymes involved in novel post-translational modifications.
  187. NPLB: Learn de novo promoter architectures from genome-wide transcription start sites.
  188. NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection.
  189. Onco-Regulon: An integrated database and software suite for site specific targeting of transcription factors of cancer genes.
  190. OncomiRdbB: a comprehensive database of microRNAs and their targets in breast cancer.
  191. OneG: a computational tool for predicting cryptic intermediates in the unfolding kinetics of proteins under native conditions.
  192. OPSID: Soft computing model for optimized siRNA design by identifying off target possibilities using artificial neural network model.
  193. PALI: a database of Phylogeny and ALIgnment of homologous protein structures.
  194. Pancreatic Cancer Database: an integrative resource for pancreatic cancer.
  195. PASS2: an automated database of protein alignments organised as structural superfamilies.
  196. PASS2 version 4: an update to the database of structure:based sequence alignments of structural domain superfamilies.
  197. PASS2.5: Database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features.
  198. PathBuilder: open source software for annotating and developing pathway resources.
  199. PCOSKB: A KnowledgeBase on genes, diseases, ontology terms and biochemical pathways associated with PolyCystic Ovary Syndrome.
  200. PcSM: Capturing native/native like structures with a physicochemical metric (pcSM) in protein folding.
  201. PDBparam: Online Resource for Computing Structural Parameters of Proteins.
  202. PeptideMine: a webserver for the design of peptides for protein:peptide binding studies derived from protein:protein interactomes.
  203. PfalDB: an integrated drug target and chemical database for Plasmodium falciparum.
  204. PhosNetConstruct: Deciphering kinase:substrate relationships by analysis of domain:specific phosphorylation network.
  205. PHPT Registry: Primary hyperparathyroidism: insights from the Indian PHPT registry.
  206. PIMADb: A Database of Protein-Protein Interactions in Huge Macromolecular Assemblies.
  207. piRNABank: a web resource on classified and clustered Piwi:interacting RNAs.
  208. piRNAQuest: searching the piRNAome for silencers.
  209. PlantRGS: a web server for the identification of most suitable candidate reference genes for quantitative gene expression studies in plants.
  210. Plasma Proteome Database: a resource for proteomics research.
  211. PLecDom: a program for identification and analysis of plant lectin domains.
  212. PLIC: protein:ligand interaction clusters.
  213. PmiRExAt: Plant miRNA expression atlas database and web applications.
  214. PocketAlign: a novel algorithm for aligning binding sites in protein structures.
  215. PocketAnnotate: towards site:based function annotation.
  216. PocketDepth: a new depth based algorithm for identification of ligand binding sites in proteins.
  217. POEAS: Automated Plant Phenomic Analysis Using Plant Ontology.
  218. PPDB: A Tool for Investigation of Plants Physiology Based on Gene Ontology.
  219. PPDB : A tool for investigation of plants physiology based on gene ontology.
  220. PPIMpred: A web server for high-throughput screening of small molecules targeting protein-protein interaction.
  221. PPS: A computing engine to find Palindromes in all Protein sequences.
  222. PpTFDB: A pigeonpea transcription factor database for exploring functional genomics in legumes.
  223. PRDBv2: A non-redundant protein-RNA docking benchmark version 2.0.
  224. PrediQt-Cx: post treatment health related quality of life prediction model for cervical cancer patients.
  225. PreDOSS: A computational approach for prediction of donor splice sites with improved accuracy.
  226. PreFRP: Prediction and visualization of fluctuation residues in proteins.
  227. PRIGSA: protein repeat identification by graph spectral analysis.
  228. ProInflam: A webserver for the prediction of proinflammatory antigenicity of peptides and proteins.
  229. PromBase: a web resource for various genomic features and predicted promoters in prokaryotic genomes.
  230. PromBase: High quality annotation of promoter regions for 913 bacterial genomes.
  231. ProNormz: an integrated approach for human proteins and protein kinases normalization.
  232. ProRegIn: a regularity index for the selection of native like tertiary structures of proteins.
  233. ProSTRIP: A method to find similar structural repeats in three:dimensional protein structures.
  234. ProTSAV: A protein tertiary structure analysis and validation server.
  235. ProtVirDB: a database of protozoan virulent proteins.
  236. PsRNA: a computing engine for the comparative identification of putative small RNA locations within intergenic regions.
  237. PSST2.0: Protein Data Bank Sequence Search Tool.
  238. PUFAS: An Approach to Function Annotation for Proteins of Unknown Function (PUFs) in the Transcriptome of Indian Mulberry.
  239. PVSUP: Supervised learning classification models for prediction of plant virus encoded RNA silencing suppressors.
  240. PvTFDB: A Phaseolus vulgaris transcription factors database for expediting functional genomics in legumes.
  241. QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice.
  242. QSPPRED: Prediction and analysis of quorum sensing peptides based on sequence features.
  243. QuadBase: Genome wide database of G4 DNA:occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes.
  244. Ramachandran plot: Ramachandran plot on the web
  245. RAmiRNA: Software suite for generation of SVMbased prediction models of mature miRNAs.
  246. RCDB: Renal Cancer Gene Database.
  247. riboscan: An efficient pHMM-based web-server to detect riboswitches in genomic sequences.
  248. RiceSRTFDB: a database of rice transcription factors containing comprehensive expression, cis:regulatory element and mutant information to facilitate gene function analysis.
  249. RiPPMiner: A bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links.
  250. RM2TS: From Ramachandran Maps to Tertiary Structures of Proteins.
  251. RNABP COGEST: a resource for investigating functional RNAs.
  252. RStrucFam: A web server to associate structure and cognate RNA for RNA-binding proteins from sequence information.
  253. RV-Typer: A Web Server for Typing of Rhinoviruses Using Alignment-Free Approach.
  254. Sanjeevini: a freely accessible web:server for target directed lead molecule discovery.
  255. SBSPKS: structure based sequence analysis of polyketide synthases.
  256. SBSPKSv2: Structure-based sequence analysis of polyketide synthases and non-ribosomal peptide synthetases.
  257. SEARCHGTr: a program for analysis of glycosyltransferases involved in glycosylation of secondary metabolites.
  258. Seed ProNutra Care: A tool for characterization of seed storage proteins and database of bioactive peptides having potential health benefits.
  259. SeeHaBITaT: A server on bioinformatics applications for Tospoviruses and other species.
  260. SEM (Symmetry Equivalent Molecules): A web based GUI to generate and visualize the macromolecules.
  261. SeriPort: A comprehensive view of the web-resources related to sericulture.
  262. SigMol: Repertoire of quorum sensing signaling molecules in prokaryotes.
  263. siRNAmod: A database of experimentally validated chemically modified siRNAs.
  264. SMBMDb: First whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications.
  265. SMEpred workbench: A web server for predicting efficacy of chemicallymodified siRNAs.
  266. SMS 2.0: an updated database to study the structural plasticity of short peptide fragments in non:redundant proteins.
  267. SPEER-SERVER: a web server for prediction of protein specificity determining sites.
  268. SPIDBAR: Identification of species based on DNA barcode using k-mer feature vector and Random forest classifier.
  269. SSEP2.0: Secondary Structural Elements of Proteins.
  270. SSPRED: A statistical approach for 5 splice site prediction using short sequence motifs and without encoding sequence data.
  271. SSPred: A prediction server based on SVM for the identification and classification of proteins involved in bacterial secretion systems.
  272. 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.
  273. Streptococcus pneumoniae Genome Database (SPGDB): a database for strain specific comparative analysis of Streptococcus pneumoniae genes and proteins.
  274. SUPFAM: a database of sequence superfamilies of protein domains.
  275. SUPFAM: implications for structural genomics and function annotation in genomes.
  276. SVMPBPred: SVM based protein block prediction method using sequence profiles and secondary structures.
  277. TaxKB: A knowledge base for new taxane-related drug discovery.
  278. Tbvar: A comprehensive genome variation resource for Mycobacterium tuberculosis.
  279. TFIS: A Tool for Detection of Transcription Factor Binding Sites.
  280. The Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail for zebrafish gene annotation.
  281. THGS: a web:based database of Transmembrane Helices in Genome Sequences.
  282. TiD: Standalone software for mining putative drug targets from bacterial proteome.
  283. TIPMaP: a web server to establish transcript isoform profiles from reliable microarray probes.
  284. TMC-SNPdb:: An Indian germline variant database derived from whole exome sequences.
  285. Tomato genomic resources database: an integrated repository of useful tomato genomic information for basic and applied research.
  286. TPACM4: A fast empirical GAFF compatible partial atomic charge assignment scheme for modeling interactions of small molecules with biomolecular targets.
  287. TRABAS: a database for transcription regulation by ABA signaling.
  288. TRIPATH: A Biological Genetic and Genomic Database of Three Economically Important Fungal Pathogen of Wheat :
  289. VDAP-GUI: A user-friendly pipeline for variant discovery and annotation of raw next-generation sequencing data.
  290. VIRmiRNA: a comprehensive resource for experimentally validated viral miRNAs and their targets.
  291. VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA.
  292. VIRsiRNApred: a web server for predicting inhibition efficacy of siRNAs targeting human viruses.
  293. VirulentPred: a SVM based prediction method for virulent proteins in bacterial pathogens.
  294. VPDB: Viral Protein Structural Database.
  295. WebFARM: web server for finite automated restriction mapping.
  296. WebGeSTer DB: a transcription terminator database.
  297. WildSilkbase: an EST database of wild silkmoths.
  298. WNV Typer: a server for genotyping of West Nile viruses using an alignment:free method based on a return time distribution.
  299. WPC: A supervised weighted similarity measure for gene expressions using biological knowledge.
  300. zf-IncRNApedia: A Comprehensive Online Resource for Zebrafish Long Non-Coding RNAs.
  301. ZifBASE: a database of zinc finger proteins and associated resources.
  302. ZiFPredict: a web tool for predicting DNA binding specificity in C2H2 zinc finger proteins.