Proteome Annotation


jQuery UI Tabs - Default functionality In past large number of software and web servers have been developed for annotating proteomes. This page maintain software/severs available at OSDDlinux useful in annotating proteome at protein or residue level. In OSDDlinux we have divided these packages in categories i) All for all type ofsoftware, ii) Webservers for web services, iii) Galaxy for software integated in Galaxy, iv) GUI for graphics based software, v) Third for software not belongs to Raghava's group

Software nameDescription
APSSP2Advanced Protein Secondary Structure Prediction Server
PROCLASSPrediction of Protein Structure Classification
PSAAnalysis of Protein Sequence and Multiple Alignment
BetatPred2Prediction of betaturns in proteins
CHpredictPrediction of CH..O and CH..Pi interactions
AR_NHPredPrediction of aromatic backbone NH interaction in proteins
TBBPredPrediction of Transmembrane Beta Barrel in Proteins
BetaTurnsPrediction of betaturn types in protein
BhairPredPrediction of Beta Hairpins
GammaPredPrediction of Gamma turns in protein
AlphaPredPrediction of Alpha turns in protein
PepStr3D structure prediction of bioactive peptides
SarPredA neural network based method predicts the real value of surface acessibility (SA) by using multiple sequence alignment
NRpredA server for classification of nuclear receptors
GPCRpredPrediction of families and subfamilies of G-protein coupled receptors
GPCRsclassClassification of amine type of G-protein-coupled receptors
ESLpredESLpred: SVM Based Method for Subcellular Localization of Eukaryotic Proteins
PSLpredPrediction of subcellular localization of bacterial proteins
BTXpredPrediction of Bacterial Toxins
MitpredPrediction of mitochondrial proteins using support vector machine and hidden Markov model
SRTpredSVM-based method for the classification of protein sequence as secretory or non-secretory protein
OxypredPrediction of the oxygen-binding proteins
VGIchanVoltage gated ion channel prediction server
HSLpredHSLpred: A server for the prediction of the subcellular localization of human protein
GSTpredPrediciton of Glutathione S-transferase protein
NTXpredPrediction of Neurotoxins and its source and probable function from primary amino acid sequence
VICMpredPrediction of Virulence factors, Information molecule, Cellular process and Metabolism molecule in the Bacterial proteins
ALGpredPrediction of allergenic proteins and mapping of IgE epitopes
PseaPredPrediction of proteins secreted by malarial parasite P.falciparum into infected-erythrocyte
RSLPredA SVM based method for subcellular localization prediction of rice proteins
ESLPred2ESLpred2 is an improved version of ESLpred, for predicting eukaryotic sub cellular localization
ChemoPredA tool to predict chemokine and their receptor
PFMpredPredicting mitochondrial proteins of P.falciparum
TBPredSupport Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs
ProPrintPrediction of physical or functional interactions between protein molecules
ISSpredIntein Splice Site Prediction
MangoPrediction of Protein Function from Manually Annotated proteins based on GO (Gene Ontology)
Cancer_PredA method for the prediction of Cancer lectins
LGEpredCorrelation Analysis and Prediction of Genes Expression from Amino Acid Sequence of Proteins
DNAsizeComputation of size of DNA and Protein Fragments from Their Electrophoretic Mobility
CyclinPredA SVM based prediction method to identify novel cyclins
PseaPred2Prediction of plasmodium secretory and infected erythrocyte associated proteins
ChloroPredA web based tool for prediction of chloroplast proteins
COPidComposition Based Protein Identification
SubMitpredPrediction of Submitochondrial Location of mitochondrial Proteins
ATPintPrediction of ATP interacting protein residues
ADPintPrediction of ADP interacting protein residues
FADpredA webserver for the prediction of FAD interacting residues
GTPbinderPrediction of GTP interacting residues, dipeptides and tripeptides in a protein from its evolutionary information
NADbinderPrediction of NAD interacting residues in proteins
PreMieRA webserver for the prediction of Mannose Interacting residue
PprintA tool for predicting RNA-binding residues of a protein
GlycoPPA webserver for predicting potential N-and O-glycosites in prokaryotic protein sequence(s)
GlycoEPIn silico platform for prediction of N-, O- and C-Glycosites in eukaryotic protein sequences
tRNAmodPrediction of transfer RNA (tRNA) modifications
VitaPredPrediction method for the vitamin-interacting residues in protein sequences
RNApinSupport Vector Machines (SVMs) based web-server for the prediction of Protein Interacting Nucleotides (PINs) in RNA sequences
RNAintA tool for the prediction of RNA interacting mono-residues (RIMRs), di-residues (RIDRs), tri-residues (RITRs), tetra-residues (RITTRs) and penta-residues (RIPRs) from protein sequences
DNAintPrediction of DNA interacting residues (DIRs) from protein sequences
DOMprintDomain-domain interaction prediction server
MYCOprintMycobacterial protein-protein interaction predictor
AntAn algorithm for multiple sequence alignment.
AvogadroAvogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.
Blast+BLAST finds regions of local similarity between sequences
blast2goBlast2GO is an ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data.
CD-HITPrograms designed to quickly align and group sequences.
ClustalxClustalX: This version has a graphical user interface for clustax.
Cn3dCn3D is a structure and sequence alignment viewer for NCBI databases that allows viewing of 3-D structures along with sequence and structure
ConCavityConCavity identifies binding pockets by combining sequence conservation and pocket information.
CytoscapePlatform for visualizing complex-networks and integrating these with attribute data.
DESMONDDESMOND is developed to perform high-speed molecular dynamics simulations of biological systems on conventional computer clusters.
EMBOSS completeEuropean molecular biology open software suite. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web.
Garlica free molecular visualization program
GROMACSProfile hidden Markov models for protein sequence analysis.
HMMERBiosequence analysis using profile hidden Markov Models.
JalviewA Java multiple alignment editor.
JMolOpen source molecule viewer written in Java. It runs as a standalone application and as a web browser applet.
MEME/MASTSearch for common motifs in DNA or protein sequences.
MERCISoftware to find motif in proteins and peptides.
MGLToolsFor visualization and analysis of molecular structures.
ModellerMODELLER is used for homology or comparative modeling of protein three-dimensional structures.
MOPACMOPAC (Molecular Orbital PACkage) is a semiempirical quantum chemistry program based on Dewar and Thiel's NDDO approximation.
MUMMERMUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.
PyMOLMolecular visualization program with high quality image output.
RaccoonRaccoon is a graphical interface for preparing AutoDock virtual screenings.
RasMolRandomized Axelerated Maximum Likelihood of phylogenetic trees.
ReadseqConverts amino acid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others.
ViewmolAn open-source graphical front end for computational chemistry programs such as Gaussian, Gamess, and Mopac.

Software nameDescription
APSSP2Advanced Protein Secondary Structure Prediction Server
PROCLASSPrediction of Protein Structure Classification
PSAAnalysis of Protein Sequence and Multiple Alignment
BetatPred2Prediction of betaturns in proteins
CHpredictPrediction of CH..O and CH..Pi interactions
AR_NHPredPrediction of aromatic backbone NH interaction in proteins
TBBPredPrediction of Transmembrane Beta Barrel in Proteins
BetaTurnsPrediction of betaturn types in protein
BhairPredPrediction of Beta Hairpins
GammaPredPrediction of Gamma turns in protein
AlphaPredPrediction of Alpha turns in protein
PepStr3D structure prediction of bioactive peptides
SarPredA neural network based method predicts the real value of surface acessibility (SA) by using multiple sequence alignment
NRpredA server for classification of nuclear receptors
GPCRpredPrediction of families and subfamilies of G-protein coupled receptors
GPCRsclassClassification of amine type of G-protein-coupled receptors
ESLpredESLpred: SVM Based Method for Subcellular Localization of Eukaryotic Proteins
PSLpredPrediction of subcellular localization of bacterial proteins
BTXpredPrediction of Bacterial Toxins
MitpredPrediction of mitochondrial proteins using support vector machine and hidden Markov model
SRTpredSVM-based method for the classification of protein sequence as secretory or non-secretory protein
OxypredPrediction of the oxygen-binding proteins
VGIchanVoltage gated ion channel prediction server
HSLpredHSLpred: A server for the prediction of the subcellular localization of human protein
GSTpredPrediciton of Glutathione S-transferase protein
NTXpredPrediction of Neurotoxins and its source and probable function from primary amino acid sequence
VICMpredPrediction of Virulence factors, Information molecule, Cellular process and Metabolism molecule in the Bacterial proteins
ALGpredPrediction of allergenic proteins and mapping of IgE epitopes
PseaPredPrediction of proteins secreted by malarial parasite P.falciparum into infected-erythrocyte
RSLPredA SVM based method for subcellular localization prediction of rice proteins
ESLPred2ESLpred2 is an improved version of ESLpred, for predicting eukaryotic sub cellular localization
ChemoPredA tool to predict chemokine and their receptor
PFMpredPredicting mitochondrial proteins of P.falciparum
TBPredSupport Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs
ProPrintPrediction of physical or functional interactions between protein molecules
ISSpredIntein Splice Site Prediction
MangoPrediction of Protein Function from Manually Annotated proteins based on GO (Gene Ontology)
Cancer_PredA method for the prediction of Cancer lectins
LGEpredCorrelation Analysis and Prediction of Genes Expression from Amino Acid Sequence of Proteins
DNAsizeComputation of size of DNA and Protein Fragments from Their Electrophoretic Mobility
CyclinPredA SVM based prediction method to identify novel cyclins
PseaPred2Prediction of plasmodium secretory and infected erythrocyte associated proteins
ChloroPredA web based tool for prediction of chloroplast proteins
COPidComposition Based Protein Identification
SubMitpredPrediction of Submitochondrial Location of mitochondrial Proteins
ATPintPrediction of ATP interacting protein residues
ADPintPrediction of ADP interacting protein residues
FADpredA webserver for the prediction of FAD interacting residues
GTPbinderPrediction of GTP interacting residues, dipeptides and tripeptides in a protein from its evolutionary information
NADbinderPrediction of NAD interacting residues in proteins
PreMieRA webserver for the prediction of Mannose Interacting residue
PprintA tool for predicting RNA-binding residues of a protein
GlycoPPA webserver for predicting potential N-and O-glycosites in prokaryotic protein sequence(s)
GlycoEPIn silico platform for prediction of N-, O- and C-Glycosites in eukaryotic protein sequences
tRNAmodPrediction of transfer RNA (tRNA) modifications
VitaPredPrediction method for the vitamin-interacting residues in protein sequences
RNApinSupport Vector Machines (SVMs) based web-server for the prediction of Protein Interacting Nucleotides (PINs) in RNA sequences
RNAintA tool for the prediction of RNA interacting mono-residues (RIMRs), di-residues (RIDRs), tri-residues (RITRs), tetra-residues (RITTRs) and penta-residues (RIPRs) from protein sequences
DNAintPrediction of DNA interacting residues (DIRs) from protein sequences
DOMprintDomain-domain interaction prediction server
MYCOprintMycobacterial protein-protein interaction predictor

Software nameDescription
BetatPred2Usage: betatpred2.pl -i /gpsr/examples/example.fasta -o out.betatpred2
CHpredictUsage: chpredict.pl -i /gpsr/examples/example_chpredict.fasta -o out.chpredict
AR_NHPredUsage: ar_nhpred.pl -i /gpsr/examples/example.fasta -o out.ar_nhpred
TBBPredUsage: tbbpred.pl -i /gpsr/examples/example.fasta -m 3 -t 0 -o out.tbbpred
BetaTurnsUsage: betaturns.pl -i /gpsr/examples/example.fasta -o out.betaturns
BhairPredUsage: bhairpred.pl -i /gpsr/examples/example.fasta -t 0 -o out.bhairpred
GammaPredUsage: gammapred.pl -i /gpsr/examples/example.fasta -o out.gammapred
AlphaPredUsage: alphapred.pl -i /gpsr/examples/example.fasta -o out.alphapred
PepStrUsage: pepstr.pl -i /gpsr/examples/example_pepstr.fasta -e 1 -o out.pdb
SarPredUsage: sarpred.pl -i /gpsr/examples/example.fasta -o out.sarpred
NRpredUsage: : propred1.pl -i input file -o output
GPCRpredUsage: : gpcrpred.pl -i input file -o output
GPCRsclassUsage: : gpcrsclass.pl -i input file -o output
ESLpredUsage: : eslpred.pl -i input file -o output
PSLpredUsage: : pslpred.pl -i input file -o output
BTXpredUsage:perl btxpred.pl -i fasta_file -o out_file -m type for prediction -a approach
SRTpredUsage:perl srtpred.pl -i fasta_file -t threshold -m method -o output_file
HSLpredUsage: hslpred.pl -i /gpsr/examples/example.fasta -o out.hslpred
GSTpredUsage: gstpred.pl -i /gpsr/examples/example.fasta -t 0.2 -m 1 -o out.gstpred
NTXpredUsage: ntxpred.pl -i /gpsr/examples/example_ntxpred.fasta -m 1 -o out.ntxpred
RSLPredUsage:perl rslpred.pl -i fasta_file -o out_file -m model selected
ESLPred2Usage: ./eslpred2.pl -i fasta_file -o out_file
ChemoPredUsage:perl chempred.pl -i sequence_file -o out_file -t thres -m model
TBPredUsage: tbpredmain.pl -i /gpsr/examples/example.fasta -o out.tbpred
Cancer_PredUsage:perl cancerpred.pl -i fasta_file (Single protein only) -o out_file -t thres
PseaPred2Usage: pseapred.pl -i /gpsr/examples/example.fasta -a 1 -t 0 -o out.pseapred
ATPintUsage:perl atpint.pl -i fasta_file -o output_fil
FADpredUsage:perl fadpred.pl -i fasta_file -t threshold -m method -o output_file
GTPbinderUsage: ./gtpbinder.pl -i fasta_file -t threshold -m method -o output_file
NADbinderUsage:perl nadbinder.pl -i fasta_file -t threshold -o output_file
PreMieRUsage: premier.pl -i /gpsr/examples/example.fasta -t 0 -o out.premier
Pprint Usage: pprint.pl -i /gpsr/examples/example.fasta -t 0 -o out.pprint
GlycoPPUsage: glycopp.pl -i /gpsr/examples/example.fasta -t 0 -m 1 -o out.glycopp
GlycoEPUsage: glycoep.pl -i /gpsr/examples/example.fasta -t 0 -m 1 -o out.glycoep
tRNAmodUsage: : perl trnamod.pl -i input_tRNA_fasta_file -t threshold -o output_file -s source(ALL/A/B/E/EC/EM/EP/V) -p approach(hybrid/binary)
VitaPredUsage: perl vitapred.pl -i input_protein_fasta_file -t threshold -o output_file -a approach(1/2) -m method(1/2/3/4)
RNApinUsage: ./rnapin.pl -i /gpsr/examples/example_rnapin.fasta -t 0 -o out.rnapin
RNAintUsage: perl rnaint.pl -i input_protein_fasta_file -t threshold -o output_file -a approach(1/2/3/4/5)

Software nameDescription
PepStr 3D structure prediction of bioactive peptides
AlphaPred Prediction of Alpha turns in protein
APSSP2 Advanced Protein Secondary Structure Prediction Server
AR_NHPred Prediction of aromatic backbone NH interaction in proteins
TBBPred Prediction of Transmembrane Beta Barrel in Proteins
BetatPred Prediction of betaturns in proteins
BetatPred2 Prediction of betaturns in proteins
BetaTurnsPrediction of betaturn types in protein
BhairPred Prediction of Beta Hairpins
CHpredict Prediction of CH..O and CH..Pi interactions
Gammapred Prediction of Gamma turns in protein
SARpred A neural network based method predicts the real value of surface acessibility (SA) by using multiple sequence alignment
NRpredA server for classification of nuclear receptors
ESLpredSVM Based Method for Subcellular Localization of Eukaryotic Proteins
PSLpredPrediction of subcellular localization of bacterial proteins
BTXpred Prediction of Bacterial Toxins
GPCRsclassClassification of amine type of G-protein-coupled receptors
SRTpredSVM-based method for the classification of protein sequence as secretory or non-secretory protein
HSLpredA server for the prediction of the subcellular localization of human protein
GSTpredPrediciton of Glutathione S-transferase protein
GlycoppA webserver for predicting potential N-and O-glycosites in prokaryotic protein sequence(s)
GlycoepIn silico platform for prediction of N-, O- and C-Glycosites in eukaryotic protein sequences
NTXpredPrediction of Neurotoxins and its source and probable function from primary amino acid sequence
VICMpredPrediction of Virulence factors, Information molecule, Cellular process and Metabolism molecule in the Bacterial proteins
ALGpredPrediction of allergenic proteins and mapping of IgE epitopes
PseaPredPrediction of proteins secreted by malarial parasite P.falciparum into infected-erythrocyte
RSL-PredA SVM based method for subcellular localization prediction of rice proteins
IssPredIntein Splice Site Prediction
TBPredSupport Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs
PROprintPrediction of physical or functional interactions between protein molecules
Hivcopred Server for prediction of HIV coreceptor usage

Software nameDescription
AvogadroAvogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.
CytoscapePlatform for visualizing complex-networks and integrating these with attribute data.
GarlicA free molecular visualization program.
JalviewA Java multiple alignment editor.
JmolOpen source molecule viewer written in Java. It runs as a standalone application and as a web browser applet.
PyMolMolecular visualization program with high quality image output.
RaccoonRaccoon is a graphical interface for preparing AutoDock virtual screenings.
RasMolRasMol is a computer program written for molecular graphics visualization

Software nameDescription
AntAn algorithm for multiple sequence alignment.
AvogadroAvogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.
CD-HITPrograms designed to quickly align and group sequences.
ClustalxClustalX: This version has a graphical user interface for clustax.
ConCavityConCavity identifies binding pockets by combining sequence conservation and pocket information.
Cn3dCn3D is a structure and sequence alignment viewer for NCBI databases that allows viewing of 3-D structures along with sequence and structure
CytoscapePlatform for visualizing complex-networks and integrating these with attribute data.
DESMONDDESMOND is developed to perform high-speed molecular dynamics simulations of biological systems on conventional computer clusters.
EMBOSS completeEuropean molecular biology open software suite. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web.
Garlica free molecular visualization program
GROMACSProfile hidden Markov models for protein sequence analysis.
HMMERBiosequence analysis using profile hidden Markov Models.
JalviewA Java multiple alignment editor.
JMolOpen source molecule viewer written in Java. It runs as a standalone application and as a web browser applet.
MEME/MASTSearch for common motifs in DNA or protein sequences.
MERCISoftware to find motif in proteins and peptides.
MGLToolsFor visualization and analysis of molecular structures.
ModellerMODELLER is used for homology or comparative modeling of protein three-dimensional structures.
MOPACMOPAC (Molecular Orbital PACkage) is a semiempirical quantum chemistry program based on Dewar and Thiel's NDDO approximation.
MUMMERMUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.
PyMOLMolecular visualization program with high quality image output.
RaccoonRaccoon is a graphical interface for preparing AutoDock virtual screenings.
RasMolRandomized Axelerated Maximum Likelihood of phylogenetic trees.
ReadseqConverts amino acid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others.
ViewmolAn open-source graphical front end for computational chemistry programs such as Gaussian, Gamess, and Mopac.