3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.



DOMAC is an accurate, protein domain prediction server that integrates homology modeling, domain parsing, and ab initio methods together.



EVALLER predicts potential protein allergenicity from primary amino acid sequence.



FastContact is a free energy scoring tool for protein-protein complex structures.



FGF (Fishing Gene Family) is a resource for finding gene families given a set of protein sequences by investigating phylogenetic trees, duplication fate, and selective pressure (ka/ks calculations).



PAR-3D (Protein Active site Residues - 3D structural motif) uses a structure-based approach for predicting function. Using 3D structural motifs defined for different classes of proteases, glycolytic pathway enzymes and metal-binding sites, PAR-3D predicts probable active site residues.



iPDA (Integrated Protein Disorder Analyzer) predicts disordered regions of a query protein sequence.



MOLPROBITY is a structure validation program that can calculate and display steric, H-bonding, and van der Waals interactions for 3D structures of proteins, nucleic acids, and complexes. is a protein structure prediction meta server that provides automated tools for protein structure prediction and analysis using a consensus approach.



Phobius is a combined transmembrane topology and signal peptide predictor. The server also allows for constrained and homology-enriched predictions.



PI2PE (Protein Interface/Interior Prediction Engine) consists of three predictors (WESA, cons-PPISP, and DISPLAR) for predicting solvent accessibility and interface residues from the structure of a protein-binding or DNA-binding protein.



Protein Interactions Calculator (PIC) is a server which recognizes various kinds of interactions; such as disulphide bonds, hydrophobic interactions, hydrogen bonds, aromatic interactions, and ionic interactions within a protein or between proteins in a complex.



PrDOS (Protein Disorder Prediction Server) is a server to predict the disordered regions of a protein from its amino acid sequence.



ProSA-web (Protein Structure Analysis) is an extension of the classic ProSA program used for the refinement and validation of experimental protein structures and in structure prediction and modeling.



RNABindR is a server for analyzing and predicting RNA binding sites in proteins.



SH3-Hunter identifies putative SH3 domain interaction sites on protein sequences.



SiteFINDER|3D predicts functionally important regions in proteins of known structure using conserved functional group (CFG) analysis.



SLiMDisc (Short Linear Motif Discovery) is a tool for finding shared motifs in proteins with a common attribute such as sub-cellular location or a common interaction partner.



The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool that is more accurate than ClustalW for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. PROTOGENE turns amino acid alignments into CDS nucleotide alignments. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods.



WoLF PSORT is an extension of the PSORT II program for protein subcellular location prediction.



ZiFiT (Zinc Finger Targeter) assists in the design of zinc finger proteins that can bind to specific DNA sequences; free registration is required.


Protein Structural Classes :

It predict weather protein belong to class Alpha or Beta or Alpha+Beta or Alpha/Beta.



RPFOLD server allows to predict top 5 similar fold in PDB (Protein DataBank) for a ginen protein sequence (query)


Prediction of Beta Turns in Proteins using Neural Network and multiple alignment techniques. This is highly accurate method for beta turn prediction.



Transmembrane Beta Barrel prediction server predicts the transmembrane Beta barrel regions in a given protein sequence. The server uses a forked strategy for predicting residues which are in transmembrane beta barrel regions. Prediction can be done based only on neural networks or based on statistical learning technique - SVM or combination of two methods



Prediction of Gamma-turns in Proteins using Multiple Alignment and Secondary Structure Information.



The Pepstr server predicts the tertiary structure of small peptides with sequence length varying between 7 to 25 residues. The prediction strategy is based on the realization that ?-turn is an important and consistent feature of small peptides in addition to regular structures.




PAT (for Protein Analysis Toolkit):


Predic Protein :








DIAL (dihedral alignment) is a server that provides access to a dynamic programming algorithm for structural alignment of RNA.



INFO-RNA is a server for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.



miPred (microRNA Predictor) can distinguish between real and pseudo microRNA precursors.



pknotsRG is a server for single sequence RNA secondary structure prediction including pseudoknots; source code, binary executable, and web service available.



RADAR (RNA Data Analysis and Research) provides multiple tools for RNA structure analysis including: pairwise structure alignment, multiple structure alignment, constrained structure alignment, database searching, and prediction of the consensus structure for a set of RNA sequences.



RNAz detects functional RNA secondary structures in multiple sequence alignments based on thermodynamic stability and structural conservation.



TFAM is a system to classify the function of tRNAs that is based on tRNA structural alignments.





G2D (Candidate Genes to Inherited Diseases) scans a human genomic region for genes related to an inherited disease. The G2D server also presents precomputed candidate genes for more than 600 genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene.


Gibbs Motif Sampler:

Gibbs Motif Sampler allows you to identify motifs, conserved regions, in DNA or protein sequences. This tool can be applied for the detection of transcription factor binding sites (TFBS).



KAAS (KEGG Automatic Annotation Server) is a tool for ortholog assignment and pathway mapping. KAAS provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database. The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways.



LTR_Finder (Long Terminal Repeat Finder) is an efficient program for finding full-length LTR retrotransposons in genome sequences.



MelinaII (Motif Elucidator in Nucleotide Sequence Assembly) can run multiple motif prediction tools (Consensus, MEME, Gibbs Sampler, MDScan, Weeder) simultaneously. Graphical results can be used to compare predictions of potential DNA motifs (such as transcription factor binding sites, TFBS) in promoter regions.



OligoCalc calculates the physical properties of single- and double-stranded DNA and RNA molecules including melting temperature (multiple methods), concentration, molecular weight, and absorbance at 260 nanometers. OligoCalc can also account for 5� and 3� chemical modifications and predict potential hairpin loop formation.



OPTIMIZER is an application that optimizes the codon usage of a DNA sequence. This server can be used to predict and optimize the level expression of a gene in heterologous gene expression systems.



VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species.



A web server for locating probable protein coding region in nucleotide sequence using fourier tranform approach (Issac, B., Singh, H., Kaur, H. and Raghava, G.P.S. (2002) Bioinformatics 18:196).



Spectral Repeat Finder (SRF) is a program to find repeats through an analysis of the power spectrum of a given DNA sequence. By repeat we mean the repeated occurrence of a segment of N nucleotides within a DNA sequence. SRF is an ab initio technique as no prior assumptions need to be made regarding either the repeat length, its fidelity, or whether the repeats are in tandem or not.


1. Ab/Ag concentartion -> This web-server allow to compute the endpoint titer and concentration of Antibody(Ab) or Antigen(Ag) from ELISA data(Raghava, G. P. S. and Agrewala, J. N. (2001) Biotech Software and Internet Report, 2:196). This server is based on graphical method developed for calculating Ab/Ag concentration (Raghava, G.P.S., Joshi, A.K. and Agrewala, J.N. (1992) J. Immunol. Methods 153, 263-264).


2. MHC Class II binding peptide -> Matrix Optimization Technique for Predicting MHC binding Core (Singh, H. and Raghava, G. P. S. (2002) Biotech Software and Internet Report, 3:146).


3. MMBPred Prediction of of MHC class I binders which can bind to wide range of MHC alleles with high affinity. This server has potential to develop sub-unit vaccine for large population (Bhasin, M., and Raghava, G.P.S. (2003) Hybridoma and Hybridomics 22: 229).


4. nHLAPred: Prediction of MHC Class I Restricted T Cell Epitopes -> This server allow to predict binding peptide for 67 MHC Class I alleles. This also allow to predict the proteasome cleavage site and binding peptide that have cleavage site at C terminus (potential T cell epitopes). This uses the hybrid approach for prediction (Neural Network + Quantitative Matrix) .


5. ProPred1: Prediction of MHC Class I binding peptide -> The aim of this server is to predict MHC Class-I binding regions in an antigen sequence (Singh, H. and Raghava, G.P.S. (2003) Bioinformatics, 19: 1009).


6. ProPred: Prediction of MHC Class II binding peptide -> The aim of this server is to predict MHC Class-II binding regions in an antigen sequence (Singh, H. and Raghava, G. P. S. (2001) Bioinformatics 17: 1236).


7. CTLPred: Direct method of prediction of CTL Epitopes in an antigen sequence. This server utlize the machine learning techniques Support Vector Machine(SVM) and Aritificial Neural Network (ANN) for prediction (Bhasin, M. and Raghava, G. P. S. (2004) Vaccine (In Press)).


8. MHCBench : It is an interface developed for evaluating the Major Histocompatibility Complex (MHC) binding peptide prediction algorithms.


9. HLADR4Pred: SVM and ANN based methods for predicting HLA-DRB1*0401 binding peptides in an Antigen Sequence (Bhasin, M. and Raghava, G.P.S. (2003) Bioinformatics 20:421).


10. TAPPred: TAPPred is an on-line service for predicting binding affinity of peptides toward the TAP transporter. The Prediction is based on cascade SVM, using sequence and properties of the the amino acids(Bhasin, M. and Raghava, G. P. S. (2004) Protein Science 13:596-607).


11. MHCBN: The MHCBN is a curated database consisting of detailed information about Major Histocompatibility Complex (MHC) Binding,Non-binding peptides and T-cell epitopes.The version 3.1 of database provides information about peptides interacting with TAP and MHC linked autoimmune diseases (Bhasin, M., Singh, H. and Raghava, G. P. S. (2003) Bioinformatics 19: 665). This databse is also launched by European Bioinformatics Institute (EBI) Hinxton, Cambridge, UK.


12. BCIPep: is collection of the peptides having the role in Humoral immunity. The peptides in the database has varying measure of immunogenicity.This database can assist in the development of method for predicting B cell epitopes, desigining synthetic vaccines and in disease diagnosis. This databse is also launched by European Bioinformatics Institute (EBI) Hinxton, Cambridge, UK.


13. BcePred: The BcePred server predict B cell epitope based on physio-chemical properties of amino acids.


14. ABCpred: server is to predict linear B cell epitope regions in an antigen sequence, using artificial neural network. This server will assist in locating epitope regions that are useful in selecting synthetic vaccine candidates, disease diagonosis and also in allergy research.


15. HaptenDB: A database of hapten  molecules which can not activate immune system but can stimulate immune response if attach with the carrier  proteins.


16. HLAPRED: A server for predicting binders for MHC class I and II alleles. It also search these predicted binders in various genomes.


17. MHC2Pred: Prediction of binders for MHC class II alleles. This allows to predict  promiscuous class binders, which can bind to large number of MHC Class II alleles.


18. Pcleavage:  This server allows server to predict  proten (Immuno and standard).



 1. BRITE Biomolecular Relations in Information Transmission and Expression.

 2. EcoCyc/MetaCyc Encyclopedia of E. coli genes and metabolism; Metabolic encyclopedia.

 3. EMP Metabolic pathways

 4. KEGG Kyoto encyclopedia of genes and genomes

 5. Biochemical Pathways Enzyme database and link to biochemical pathway map

6. Interactive Fly Biochemical pathways in Drosophila

 7. Metabolic Pathway Metabolic pathways of biochemistry

 8. Molecular interaction Kohn molecular interaction maps

9. Malaria parasite Malaria Parasite metabolic pathways

10. aMAZE Protein function and biochemical pathways project at EBI

11. PathDB Metabolic pathway information

12. UM-BBD Microbial biocatalytic reactions and biodegradation pathways primarily for xenobiotic, chemical compounds

13. WIT Function assignments to genes and the development of metabolic models

14. THCME Medical Biochemistry Descrition of several metabolic and biochemical pathways



1. Apoptosis Pathways of apoptosis at KEGG

2. BBID Database of images of biological pathways, macromolecular structures, gene families, and cellular relationships

3. BioCarta Several signalling pathways

4. BIND The biomolecular interaction network database

5. CSNDB Cell signaling networks database 

6. GeneNet Information on gene networks, groups of coordinately working genes

7. GeNet Information on functional organization of regulatory gene networks

 8. SPAD Signalling pathway database

 9. STKE Pathway information

 10. TransPath Pathways involved in the regulation of transcription factors



1. CanPredict (cancer seq. prediction):

2. Cargo (Cancer gene prediction in Human) :




2. Superdrugdatabase:






5. Psychoactive Drug Screening Program: 


6. DNA-Ligand Docking-





1. Metadb:


2. Biochemical Periodic Table:


3. Software tools from IIT:


4. IMTECH's Raghava Page:




6. Drugdesign supersite:





1. LIPS (Lipid-helix interaction):


2. CodonO (Codon usage prediction):




4. NIH Server:


5. Dock Blaster:


6. NTMG:

NTMG (N-Terminal Truncated Mutants Generator) is a tool for generating multiplex PCR primers for designing N-terminal truncated mutants.


7. Frog:

Frog (Free Online Drug Conformation) is a service aimed at generating 3D conformations for drug-like compounds starting from their 1D or 2D descriptions (smiles or sdf).


8. CPC:

CPC (Coding Potential Calculator) distinguishes protein-coding from non-coding RNAs based on the sequence features of the input transcripts.


9. CRISPRfinder:

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Finder detects this family of direct repeats found in the DNA of many bacteria and archaea.


10. DBAli:

DBAli is a database that includes a comprehensive all-against-all comparison of protein structures in the PDB database. Tools associated with the database allow users to mine this protein structure space by establishing relationships between protein structures and their functions.


11. AC2DGel: is a web server for analysis and comparison of two-dimensional electrophoresis (2-DE) Gel images. It helps in annotating the virual 2-D gel image proteins on the basis of known molecular weight andpH scales of the markers.


12. Comp2DGel: Comparison, management and access of 2D gel electrophoresis


13. DNASIZE: Computation of DNA/Protein size -> This web-server allow to compute the length of DNA or protein fragments from its electropheric mobility using a graphical method (Raghava, G. P. S. (2001) Biotech Software and Internet Report, 2:198).