IMPORTANT WEBSERVERS AND TOOLS
PI2PE : http://pipe.scs.fsu.edu/
WoLF PSORT: http://wolfpsort.org/
Protein Structural Classes : http://imtech.res.in/raghava/proclass/
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
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): http://bioserv.cbs.cnrs.fr/htbin-post/pat/new/wpat.pl
Predic Protein : http://www.predictprotein.org//main.php
Gibbs Motif Sampler: http://bayesweb.wadsworth.org/gibbs/gibbs.html
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).
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) .
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) .
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)
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) .
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) .
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.
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
THCME Medical Biochemistry Descrition of several metabolic and biochemical
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
TransPath Pathways involved in the regulation of transcription factors
CANCER RELATED SERVERS
1. CanPredict (cancer seq. prediction): http://www.cgl.ucsf.edu/Research/genentech/canpredict/
2. Cargo (Cancer gene prediction in Human) : http://bioinfo.cnio.es/cargo/cargo.html
1. DRUGINDEX: http://www.rxlist.com/script/main/hp.asp
2. Superdrugdatabase: http://bioinformatics.charite.de/superdrug/
3. PHARMAGIST: http://bioinfo3d.cs.tau.ac.il/pharma/index.html
4. LIGBASE: http://alto.compbio.ucsf.edu/ligbase/ OR http://salilab.org/ligbase-cgi/pro.cgi
5. Psychoactive Drug Screening Program: http://pdsp.med.unc.edu/
6. DNA-Ligand Docking- http://www.scfbio-iitd.res.in/dock/dnadock.jsp
ESSENTIAL WEB SOURCES
1. Metadb: http://www.neurotransmitter.net/metadb/metadb.php
2. Biochemical Periodic Table: http://umbbd.msi.umn.edu/periodic/
3. Software tools from IIT: http://www.scfbio-iitd.res.in/bioinformatics/bioinformaticssoftware.htm
4. IMTECH's Raghava Page: http://imtech.res.in/raghava/
5. CUBIC: http://cubic.bioc.columbia.edu/services/
6. Drugdesign supersite: http://www.drugdesign.org/DrugDesignWebEntries/index.html
1. LIPS (Lipid-helix interaction): http://gila.bioengr.uic.edu/lab/larisa/lips.html
2. CodonO (Codon usage prediction): http://www.sysbio.muohio.edu/CodonO/
3. PROTEIN-PROTEIN ENERGY PREDICTION: http://structure.pitt.edu/servers/fastcontact/
4. NIH Server: http://nihserver.mbi.ucla.edu/
5. Dock Blaster: http://blaster.docking.org/
6. NTMG: http://oblab.cs.nchu.edu.tw:8080/WebSDL/
7. Frog: http://bioserv.rpbs.jussieu.fr/cgi-bin/Frog
8. CPC: http://cpc.cbi.pku.edu.cn/programs/run_cpc.jsp
9. CRISPRfinder: http://crispr.u-psud.fr/Server/CRISPRfinder.php
10. DBAli: http://salilab.org/DBAli/
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).