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Protein Function

How to assign function of a newly sequenced protein is a most important task for bioinformaticians. In this module, we list servers important for assigning function of proteins from its amino acid sequence. Broadly, these servers can be divided in following categories; i) subcellular localisation ii) identification of specific class of proteins, iii) functional annotation.

Web servers for functional annotation of proteins (Raghava's Group)

  1. ApoCanD:  Database of Human Apoptotic Proteins in the context of cancer.
  2. BioTherapi: Bioinformatics for Therapeutic Peptides and Proteins.
  3. BTXpred: A server for predicting bacterial toxins.
  4. CancerPPD:  Database of anticancer peptides and proteins.
  5. CancerPred: Prediction of the cancerlectins.
  6. ChemoPred: A server to predict chemokines and their receptor
  7. ChloroPred: Prediction of chloroplast proteins.
  8. COPid: Composition based identification and classification of proteins.
  9. CytoPred: It is a webserver for prediction and classification of cytokines.
  10. DAMpro: Disease Associated Mutations in Proteins.
  11. dbEM: A Database of Epigenetic Modifiers
  12. DNAbinder: A webserver for predicting DNA-binding proteins.
  13. DPROT:SVM-based method for predicting of disordered proteins.
  14. EGFRindb: A database of EGF(Epidermal Growth Factor) receptors  (anticaner database).
  15. ESLpred: Subcellular localization of the eukaryotic proteins using dipeptide compostion and PSI-BLAST.
  16. ESLpred2: Advanced method for subcellular localization of eukaryotic proteins.
  17. GlycoEP: Prediction of C-, N- and O-glycosylation site in eukaryotic proteins. 
  18. GlycoPP: Prediction of potential N-and O-glycosites in prokaryotic proteins.
  19. GPSR: A resource for genomocs, proteomics and system biology
  20. GSTpred: SVM-based method for predicting Glutathione S-transferase protein.
  21. GWBLAST:Genome-wide sequence similarity search using BLAST.
  22. GWFASTA: Genome-wide sequence similarity search using FASTA.
  23. HMRbase: A manually curated database of hormones and their Receptors.
  24. HSLpred: Prediction of subcellular localization of human proteins with high accuracy
  25. icaars: Identification & Classification of Aminoacyl tRNA Synthetases.
  26. LGEpred: Correlation analysis and prediction of genes expression from amino acid sequence of proteins.
  27. LPIcom: Analysis and prediction of ligand protein interaction.
  28. MARSpred: Prediction of mitochondrial aminoacyl tRNA synthetases.
  29. MitPred: Prediction of mitochondrial proteins using SVM and hidden Markov model.
  30. MtbVeb: A webportal for designing vaccine against drug resistant and emerging strains of M. tuberculosis.
  31. NPpred:  A webserver for the prediction of nuclear proteins.
  32. NRpred:  A SVM based method for the classification of nuclear receptors .
  33. NTXpred: Identification of neurotoxins their source and function from primary amino acid sequence.
  34. OXDbase: A database of Biodegradative oxygenase.
  35. OXYpred: Classification and prediction of oxygen binding proteins.
  36. PFMpred: Predicting mitochondrial proteins of malaria parasite Plasmodium falciparum. 
  37. PROGLYCPROT:  Database of experimentally characterized eubacterial and archaeal glycoproteins.
  38. ProPrInt: A web-server predicts physical or functional interactions between protein molecules.
  39. PSEApred: Prediction of Plasmodium Secretory and Infected Erythrocyte Associated Proteins.
  40. PSLpred: Predict subcellular localization of prokaryotic proteins.
  41. RNApred: A webserver for the prediction of RNA binding proteins.
  42. RSLpred: A method for the subcellular localization prediction of rice proteins.
  43. SRTpred: A method for the classification of protein sequence as secretory or non-secretory protein.
  44. TBpred: A webserver  that predicts four subcellular localization of mycobacterial proteins.
  45. ToxinPred: An in silico method, which is developed to predict and design toxic/non-toxic peptides.
  46. tRNAmod: The tRNAmod is a web-server for the prediction of transfer RNA (tRNA) modifications.
  47. VGIchan: Voltage gated ion channel prediction server.
  48. VICMPpred:  Prediction of Virulence factors, Information molecule, Cellular process and Metabolism molecule in the Bacterial proteins.

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. 3PFDB+: improved search protocol and update for the identification of representatives of protein sequence domain families.
  2. APSLAP: an adaptive boosting technique for predicting subcellular localization of apoptosis protein.
  3. ARC: automated resource classifier for agglomerative functional classification of prokaryotic proteins using annotation texts.
  4. bPE toolkit: Toolkit for computational protein engineering.
  5. CARDIO-PRED: an in silico tool for predicting cardiovascular-disorder associated proteins.
  6. CELLO2GO : Protein subCELlular LOcalization Prediction with Functional Gene Ontology Annotation.
  7. Circ2Traits: a comprehensive database for circular RNA potentially associated with disease and traits.
  8. CLAP: a web:server for automatic classification of proteins with special reference to multi:domain proteins.
  9. COILCHECK+: Structural attributes for the recognition of weak and anomalous regions in coiled:coils of myosins and other motor proteins.
  10. CPAD: A Repository of Manually Curated Experimental Data on Protein and Peptide Aggregation.
  11. CyanoPhyChe: a database for physico:chemical properties structure and biochemical pathway information of cyanobacterial proteins.
  12. dEMBF: A Comprehensive Database of Enzymes of Microalgal Biofuel Feedstock.
  13. DIM-Pred: Prediction of protein disorder on amino acid substitutions.
  14. DIRProt: A computational approach for discriminating insecticide resistant proteins from non-resistant proteins.
  15. FaaPred: a SVM based prediction method for fungal adhesins and adhesin:like proteins.
  16. FAIR: A server for internal sequence repeats.
  17. FMALIGN: Improvement of alignment accuracy utilizing sequentially conserved motifs.
  18. Folding RaCe: A robust method for predicting changes in protein folding rates upon point mutations.
  19. GAP: towards almost 100 percent prediction for β:strand:mediated aggregating peptides with distinct morphologies.
  20. HPRD: Human Protein Reference Database:2009 update.
  21. HprotDB: The Halophile protein database.
  22. Human Proteome Map: A draft map of the human proteome.
  23. HypoxiaDB: a database of hypoxia:regulated proteins.
  24. iCR: a web tool to identify conserved targets of a regulatory protein across the multiple related prokaryotic species.
  25. InterProScan: InterProScan program is used for protein functional analysis.
  26. JUZBOX: a web server for extracting biomedical words from the protein sequence.
  27. Manually curated database of rice proteins: a literature based manually curated protein centric database of rice proteins.
  28. mCSM-membrane: It predicts the effects of mutations on transmembrane proteins.
  29. MIPModDB: a central resource for the superfamily of major intrinsic proteins.
  30. MirtronPred: Identification of mirtrons in rice using MirtronPred: a tool for predicting plant mirtrons.
  31. MP3: a software tool for the prediction of pathogenic proteins in genomic and metagenomic data.
  32. MPDB: Molecular Pathways Brain Database.
  33. MPGDB: Mycobacteriophage genome database.
  34. MTBPCDB: Mycobacterium tuberculosis proteome comparison database.
  35. MycoProteaseDB: Useful resource for Mycobacterium tuberculosis complex and nontuberculous mycobacterial proteases.
  36. MycoSec: A database for Mycobacterium secretome analysis:
  37. novPTMenzy: a database for enzymes involved in novel post-translational modifications.
  38. NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection.
  39. PALI: a database of Phylogeny and ALIgnment of homologous protein structures.
  40. PathBuilder: open source software for annotating and developing pathway resources.
  41. PhosNetConstruct: Deciphering kinase:substrate relationships by analysis of domain:specific phosphorylation network.
  42. Plasma Proteome Database: a resource for proteomics research.
  43. PLecDom: a program for identification and analysis of plant lectin domains.
  44. POEAS: Automated Plant Phenomic Analysis Using Plant Ontology.
  45. PPDB : A tool for investigation of plants physiology based on gene ontology.
  46. PrediSi: It is used for the prediction of signal peptides.
  47. PreFRP: Prediction and visualization of fluctuation residues in proteins.
  48. ProNormz: an integrated approach for human proteins and protein kinases normalization.
  49. ProRegIn: a regularity index for the selection of native like tertiary structures of proteins.
  50. ProtVirDB: a database of protozoan virulent proteins.
  51. PUFAS: An Approach to Function Annotation for Proteins of Unknown Function (PUFs) in the Transcriptome of Indian Mulberry.
  52. RStrucFam: A web server to associate structure and cognate RNA for RNA-binding proteins from sequence information.
  53. SecretomeP: The method queries number of other feature prediction servers to obtain information on various post-translational and localizational aspects of the protein.
  54. SSPred: A prediction server based on SVM for the identification and classification of proteins involved in bacterial secretion systems.
  55. SUPFAM: a database of sequence superfamilies of protein domains.
  56. TFIS: A Tool for Detection of Transcription Factor Binding Sites.
  57. VirulentPred: a SVM based prediction method for virulent proteins in bacterial pathogens.
  58. ZifBASE: a database of zinc finger proteins and associated resources.
  59. ZiFPredict: a web tool for predicting DNA binding specificity in C2H2 zinc finger proteins.