Proteome Annotation
Software name Description APSSP2 Advanced Protein Secondary Structure Prediction Server PROCLASS Prediction of Protein Structure Classification PSA Analysis of Protein Sequence and Multiple Alignment BetatPred2 Prediction of betaturns in proteins CHpredict Prediction of CH..O and CH..Pi interactions AR_NHPred Prediction of aromatic backbone NH interaction in proteins TBBPred Prediction of Transmembrane Beta Barrel in Proteins BetaTurns Prediction of betaturn types in protein BhairPred Prediction of Beta Hairpins GammaPred Prediction of Gamma turns in protein AlphaPred Prediction of Alpha turns in protein PepStr 3D structure prediction of bioactive peptides SarPred A neural network based method predicts the real value of surface acessibility (SA) by using multiple sequence alignment NRpred A server for classification of nuclear receptors GPCRpred Prediction of families and subfamilies of G-protein coupled receptors GPCRsclass Classification of amine type of G-protein-coupled receptors ESLpred ESLpred: SVM Based Method for Subcellular Localization of Eukaryotic Proteins PSLpred Prediction of subcellular localization of bacterial proteins BTXpred Prediction of Bacterial Toxins Mitpred Prediction of mitochondrial proteins using support vector machine and hidden Markov model SRTpred SVM-based method for the classification of protein sequence as secretory or non-secretory protein Oxypred Prediction of the oxygen-binding proteins VGIchan Voltage gated ion channel prediction server HSLpred HSLpred: A server for the prediction of the subcellular localization of human protein GSTpred Prediciton of Glutathione S-transferase protein NTXpred Prediction of Neurotoxins and its source and probable function from primary amino acid sequence VICMpred Prediction of Virulence factors, Information molecule, Cellular process and Metabolism molecule in the Bacterial proteins ALGpred Prediction of allergenic proteins and mapping of IgE epitopes PseaPred Prediction of proteins secreted by malarial parasite P.falciparum into infected-erythrocyte RSLPred A SVM based method for subcellular localization prediction of rice proteins ESLPred2 ESLpred2 is an improved version of ESLpred, for predicting eukaryotic sub cellular localization ChemoPred A tool to predict chemokine and their receptor PFMpred Predicting mitochondrial proteins of P.falciparum TBPred Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs ProPrint Prediction of physical or functional interactions between protein molecules ISSpred Intein Splice Site Prediction Mango Prediction of Protein Function from Manually Annotated proteins based on GO (Gene Ontology) Cancer_Pred A method for the prediction of Cancer lectins LGEpred Correlation Analysis and Prediction of Genes Expression from Amino Acid Sequence of Proteins DNAsize Computation of size of DNA and Protein Fragments from Their Electrophoretic Mobility CyclinPred A SVM based prediction method to identify novel cyclins PseaPred2 Prediction of plasmodium secretory and infected erythrocyte associated proteins ChloroPred A web based tool for prediction of chloroplast proteins COPid Composition Based Protein Identification SubMitpred Prediction of Submitochondrial Location of mitochondrial Proteins ATPint Prediction of ATP interacting protein residues ADPint Prediction of ADP interacting protein residues FADpred A webserver for the prediction of FAD interacting residues GTPbinder Prediction of GTP interacting residues, dipeptides and tripeptides in a protein from its evolutionary information NADbinder Prediction of NAD interacting residues in proteins PreMieR A webserver for the prediction of Mannose Interacting residue Pprint A tool for predicting RNA-binding residues of a protein GlycoPP A webserver for predicting potential N-and O-glycosites in prokaryotic protein sequence(s) GlycoEP In silico platform for prediction of N-, O- and C-Glycosites in eukaryotic protein sequences tRNAmod Prediction of transfer RNA (tRNA) modifications VitaPred Prediction method for the vitamin-interacting residues in protein sequences RNApin Support Vector Machines (SVMs) based web-server for the prediction of Protein Interacting Nucleotides (PINs) in RNA sequences RNAint A 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 DNAint Prediction of DNA interacting residues (DIRs) from protein sequences DOMprint Domain-domain interaction prediction server MYCOprint Mycobacterial protein-protein interaction predictor Ant An algorithm for multiple sequence alignment. Avogadro Avogadro 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 blast2go Blast2GO is an ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. CD-HIT Programs designed to quickly align and group sequences. Clustalx ClustalX: This version has a graphical user interface for clustax. Cn3d Cn3D is a structure and sequence alignment viewer for NCBI databases that allows viewing of 3-D structures along with sequence and structure ConCavity ConCavity identifies binding pockets by combining sequence conservation and pocket information. Cytoscape Platform for visualizing complex-networks and integrating these with attribute data. DESMOND DESMOND is developed to perform high-speed molecular dynamics simulations of biological systems on conventional computer clusters. EMBOSS complete European 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. Garlic a free molecular visualization program GROMACS Profile hidden Markov models for protein sequence analysis. HMMER Biosequence analysis using profile hidden Markov Models. Jalview A Java multiple alignment editor. JMol Open source molecule viewer written in Java. It runs as a standalone application and as a web browser applet. MEME/MAST Search for common motifs in DNA or protein sequences. MERCI Software to find motif in proteins and peptides. MGLTools For visualization and analysis of molecular structures. Modeller MODELLER is used for homology or comparative modeling of protein three-dimensional structures. MOPAC MOPAC (Molecular Orbital PACkage) is a semiempirical quantum chemistry program based on Dewar and Thiel's NDDO approximation. MUMMER MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. PyMOL Molecular visualization program with high quality image output. Raccoon Raccoon is a graphical interface for preparing AutoDock virtual screenings. RasMol Randomized Axelerated Maximum Likelihood of phylogenetic trees. Readseq Converts amino acid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others. Viewmol An open-source graphical front end for computational chemistry programs such as Gaussian, Gamess, and Mopac.
Software name Description APSSP2 Advanced Protein Secondary Structure Prediction Server PROCLASS Prediction of Protein Structure Classification PSA Analysis of Protein Sequence and Multiple Alignment BetatPred2 Prediction of betaturns in proteins CHpredict Prediction of CH..O and CH..Pi interactions AR_NHPred Prediction of aromatic backbone NH interaction in proteins TBBPred Prediction of Transmembrane Beta Barrel in Proteins BetaTurns Prediction of betaturn types in protein BhairPred Prediction of Beta Hairpins GammaPred Prediction of Gamma turns in protein AlphaPred Prediction of Alpha turns in protein PepStr 3D structure prediction of bioactive peptides SarPred A neural network based method predicts the real value of surface acessibility (SA) by using multiple sequence alignment NRpred A server for classification of nuclear receptors GPCRpred Prediction of families and subfamilies of G-protein coupled receptors GPCRsclass Classification of amine type of G-protein-coupled receptors ESLpred ESLpred: SVM Based Method for Subcellular Localization of Eukaryotic Proteins PSLpred Prediction of subcellular localization of bacterial proteins BTXpred Prediction of Bacterial Toxins Mitpred Prediction of mitochondrial proteins using support vector machine and hidden Markov model SRTpred SVM-based method for the classification of protein sequence as secretory or non-secretory protein Oxypred Prediction of the oxygen-binding proteins VGIchan Voltage gated ion channel prediction server HSLpred HSLpred: A server for the prediction of the subcellular localization of human protein GSTpred Prediciton of Glutathione S-transferase protein NTXpred Prediction of Neurotoxins and its source and probable function from primary amino acid sequence VICMpred Prediction of Virulence factors, Information molecule, Cellular process and Metabolism molecule in the Bacterial proteins ALGpred Prediction of allergenic proteins and mapping of IgE epitopes PseaPred Prediction of proteins secreted by malarial parasite P.falciparum into infected-erythrocyte RSLPred A SVM based method for subcellular localization prediction of rice proteins ESLPred2 ESLpred2 is an improved version of ESLpred, for predicting eukaryotic sub cellular localization ChemoPred A tool to predict chemokine and their receptor PFMpred Predicting mitochondrial proteins of P.falciparum TBPred Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs ProPrint Prediction of physical or functional interactions between protein molecules ISSpred Intein Splice Site Prediction Mango Prediction of Protein Function from Manually Annotated proteins based on GO (Gene Ontology) Cancer_Pred A method for the prediction of Cancer lectins LGEpred Correlation Analysis and Prediction of Genes Expression from Amino Acid Sequence of Proteins DNAsize Computation of size of DNA and Protein Fragments from Their Electrophoretic Mobility CyclinPred A SVM based prediction method to identify novel cyclins PseaPred2 Prediction of plasmodium secretory and infected erythrocyte associated proteins ChloroPred A web based tool for prediction of chloroplast proteins COPid Composition Based Protein Identification SubMitpred Prediction of Submitochondrial Location of mitochondrial Proteins ATPint Prediction of ATP interacting protein residues ADPint Prediction of ADP interacting protein residues FADpred A webserver for the prediction of FAD interacting residues GTPbinder Prediction of GTP interacting residues, dipeptides and tripeptides in a protein from its evolutionary information NADbinder Prediction of NAD interacting residues in proteins PreMieR A webserver for the prediction of Mannose Interacting residue Pprint A tool for predicting RNA-binding residues of a protein GlycoPP A webserver for predicting potential N-and O-glycosites in prokaryotic protein sequence(s) GlycoEP In silico platform for prediction of N-, O- and C-Glycosites in eukaryotic protein sequences tRNAmod Prediction of transfer RNA (tRNA) modifications VitaPred Prediction method for the vitamin-interacting residues in protein sequences RNApin Support Vector Machines (SVMs) based web-server for the prediction of Protein Interacting Nucleotides (PINs) in RNA sequences RNAint A 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 DNAint Prediction of DNA interacting residues (DIRs) from protein sequences DOMprint Domain-domain interaction prediction server MYCOprint Mycobacterial protein-protein interaction predictor
Software name Description BetatPred2 Usage: betatpred2.pl -i /gpsr/examples/example.fasta -o out.betatpred2 CHpredict Usage: chpredict.pl -i /gpsr/examples/example_chpredict.fasta -o out.chpredict AR_NHPred Usage: ar_nhpred.pl -i /gpsr/examples/example.fasta -o out.ar_nhpred TBBPred Usage: tbbpred.pl -i /gpsr/examples/example.fasta -m 3 -t 0 -o out.tbbpred BetaTurns Usage: betaturns.pl -i /gpsr/examples/example.fasta -o out.betaturns BhairPred Usage: bhairpred.pl -i /gpsr/examples/example.fasta -t 0 -o out.bhairpred GammaPred Usage: gammapred.pl -i /gpsr/examples/example.fasta -o out.gammapred AlphaPred Usage: alphapred.pl -i /gpsr/examples/example.fasta -o out.alphapred PepStr Usage: pepstr.pl -i /gpsr/examples/example_pepstr.fasta -e 1 -o out.pdb SarPred Usage: sarpred.pl -i /gpsr/examples/example.fasta -o out.sarpred NRpred Usage: : propred1.pl -i input file -o output GPCRpred Usage: : gpcrpred.pl -i input file -o output GPCRsclass Usage: : gpcrsclass.pl -i input file -o output ESLpred Usage: : eslpred.pl -i input file -o output PSLpred Usage: : pslpred.pl -i input file -o output BTXpred Usage:perl btxpred.pl -i fasta_file -o out_file -m type for prediction -a approach SRTpred Usage:perl srtpred.pl -i fasta_file -t threshold -m method -o output_file HSLpred Usage: hslpred.pl -i /gpsr/examples/example.fasta -o out.hslpred GSTpred Usage: gstpred.pl -i /gpsr/examples/example.fasta -t 0.2 -m 1 -o out.gstpred NTXpred Usage: ntxpred.pl -i /gpsr/examples/example_ntxpred.fasta -m 1 -o out.ntxpred RSLPred Usage:perl rslpred.pl -i fasta_file -o out_file -m model selected
ESLPred2 Usage: ./eslpred2.pl -i fasta_file -o out_file ChemoPred Usage:perl chempred.pl -i sequence_file -o out_file -t thres -m model TBPred Usage: tbpredmain.pl -i /gpsr/examples/example.fasta -o out.tbpred Cancer_Pred Usage:perl cancerpred.pl -i fasta_file (Single protein only) -o out_file -t thres PseaPred2 Usage: pseapred.pl -i /gpsr/examples/example.fasta -a 1 -t 0 -o out.pseapred ATPint Usage:perl atpint.pl -i fasta_file -o output_fil FADpred Usage:perl fadpred.pl -i fasta_file -t threshold -m method -o output_file GTPbinder Usage: ./gtpbinder.pl -i fasta_file -t threshold -m method -o output_file NADbinder Usage:perl nadbinder.pl -i fasta_file -t threshold -o output_file PreMieR Usage: 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 GlycoPP Usage: glycopp.pl -i /gpsr/examples/example.fasta -t 0 -m 1 -o out.glycopp GlycoEP Usage: glycoep.pl -i /gpsr/examples/example.fasta -t 0 -m 1 -o out.glycoep tRNAmod Usage: : 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) VitaPred Usage: perl vitapred.pl -i input_protein_fasta_file -t threshold -o output_file -a approach(1/2) -m method(1/2/3/4) RNApin Usage: ./rnapin.pl -i /gpsr/examples/example_rnapin.fasta -t 0 -o out.rnapin RNAint Usage: perl rnaint.pl -i input_protein_fasta_file -t threshold -o output_file -a approach(1/2/3/4/5)
Software name Description 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 BetaTurns Prediction 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 NRpred A server for classification of nuclear receptors ESLpred SVM Based Method for Subcellular Localization of Eukaryotic Proteins PSLpred Prediction of subcellular localization of bacterial proteins BTXpred Prediction of Bacterial Toxins GPCRsclass Classification of amine type of G-protein-coupled receptors SRTpred SVM-based method for the classification of protein sequence as secretory or non-secretory protein HSLpred A server for the prediction of the subcellular localization of human protein GSTpred Prediciton of Glutathione S-transferase protein Glycopp A webserver for predicting potential N-and O-glycosites in prokaryotic protein sequence(s) Glycoep In silico platform for prediction of N-, O- and C-Glycosites in eukaryotic protein sequences NTXpred Prediction of Neurotoxins and its source and probable function from primary amino acid sequence VICMpred Prediction of Virulence factors, Information molecule, Cellular process and Metabolism molecule in the Bacterial proteins ALGpred Prediction of allergenic proteins and mapping of IgE epitopes PseaPred Prediction of proteins secreted by malarial parasite P.falciparum into infected-erythrocyte RSL-Pred A SVM based method for subcellular localization prediction of rice proteins IssPred Intein Splice Site Prediction TBPred Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs PROprint Prediction of physical or functional interactions between protein molecules Hivcopred Server for prediction of HIV coreceptor usage
Software name Description Avogadro Avogadro 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. Cytoscape Platform for visualizing complex-networks and integrating these with attribute data. Garlic A free molecular visualization program. Jalview A Java multiple alignment editor. Jmol Open source molecule viewer written in Java. It runs as a standalone application and as a web browser applet. PyMol Molecular visualization program with high quality image output. Raccoon Raccoon is a graphical interface for preparing AutoDock virtual screenings. RasMol RasMol is a computer program written for molecular graphics visualization
Software name Description Ant An algorithm for multiple sequence alignment. Avogadro Avogadro 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-HIT Programs designed to quickly align and group sequences. Clustalx ClustalX: This version has a graphical user interface for clustax. ConCavity ConCavity identifies binding pockets by combining sequence conservation and pocket information. Cn3d Cn3D is a structure and sequence alignment viewer for NCBI databases that allows viewing of 3-D structures along with sequence and structure Cytoscape Platform for visualizing complex-networks and integrating these with attribute data. DESMOND DESMOND is developed to perform high-speed molecular dynamics simulations of biological systems on conventional computer clusters. EMBOSS complete European 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. Garlic a free molecular visualization program GROMACS Profile hidden Markov models for protein sequence analysis. HMMER Biosequence analysis using profile hidden Markov Models. Jalview A Java multiple alignment editor. JMol Open source molecule viewer written in Java. It runs as a standalone application and as a web browser applet. MEME/MAST Search for common motifs in DNA or protein sequences. MERCI Software to find motif in proteins and peptides. MGLTools For visualization and analysis of molecular structures. Modeller MODELLER is used for homology or comparative modeling of protein three-dimensional structures. MOPAC MOPAC (Molecular Orbital PACkage) is a semiempirical quantum chemistry program based on Dewar and Thiel's NDDO approximation. MUMMER MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. PyMOL Molecular visualization program with high quality image output. Raccoon Raccoon is a graphical interface for preparing AutoDock virtual screenings. RasMol Randomized Axelerated Maximum Likelihood of phylogenetic trees. Readseq Converts amino acid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others. Viewmol An open-source graphical front end for computational chemistry programs such as Gaussian, Gamess, and Mopac.