Standalone software of the OSDD-Linux
In this genomic era, standalone (command-line) bioinformatics tools are helpful for analyzing large-scale data. Therefore, to meet the demand of these standalone tools, in OSDD-Linux we are providing standalone versions of all the methods. It also maintains the privacy of user's data and results. These standalones software are very user-friendly and user can run them by little exposure of linux (It doest not require expertise). By simple execution of program on the terminal (e.g. perl betaturns.pl) will display the usage (e.g. ./betaturns.pl -i /gpsr/examples/example.fasta -o out.betaturns) or help document.
Name of standalone main program Applications APSSP2 apssp2.pl Advanced Protein Secondary Structure Prediction Server PROCLASS proclass.pl Prediction of Protein Structure Classification PSA Analysis of Protein Sequence and Multiple Alignment BetatPred2 betatpred2.pl Prediction of betaturns in proteins CHpredict chpredict.pl Prediction of CH..O and CH..Pi interactions AR_NHPred ar_nhpred.pl Prediction of aromatic backbone NH interaction in proteins TBBPred tbbpred.pl Prediction of Transmembrane Beta Barrel in Proteins BetaTurns betaturns.pl Prediction of betaturn types in protein BhairPred bhairpred.pl Prediction of Beta Hairpins GammaPred gammapred.pl Prediction of Gamma turns in protein AlphaPred alphapred.pl Prediction of Alpha turns in protein PepStr pepstr.pl 3D structure prediction of bioactive peptides SarPred sarpred.pl A neural network based method predicts the real value of surface acessibility (SA) by using multiple sequence alignment FiSipred fisipred.pl Prediction of backbone torsion angles phi and psi
Epitope based Vaccines
PROPRED1 propred1.pl prediction of promiscuous MHC Class-I binding sites nHLA4pred nhlapred.pl A neural network based MHC Class-I Binding Peptide Prediction Server MMBpred Prediction of mutated high affinity and promiscuous MHC class-I binding peptides from protein sequence Pcleavage pcleavage.pl An SVM based method for proteosome cleavage prediction TAPpred tappred.pl TAPPred is a tool for predicting binding affinity of peptides toward the TAP transporter CTLpred ctlpred.pl CTLpred: Prediction of cytotoxic T cell epitopes PROPRED propred.pl Prediction of HLA-DR binding sites HLADR4pred hladr4pred.pl SVM based method for predicting HLA-DRB1 binding peptides in an antigen sequence CBtope Conformational B-cell epitope prediction LBtope Prediction of linear B-cell epitopes MHC2pred SVM based method for prediction of promiscuous MHC class II binding peptides MHC mhc.pl Matrix Optimization Technique for Predicting MHC binding Core MHCbench mhcbench.pl Evaluation of Major Histocompatibility Complex (MHC) binding peptide prediction algorithms BCEpred bcepred.pl Bcepred: Prediction of linear B-cell epitopes, using physico-chemical properties ABCpred abcpred.pl Prediction of B-cell epitopes in antigen sequence HLApred HLA_affi FDR4 Prediction of binding affinity of peptide binders in an antigenic sequence for a MHC class II allele HLA-DRB1*0401 Tmhcpred Prediction of MHC Class I and II binding peptides IFNepitope ifnepitope.pl A server for predicting and designing interferon-gamma inducing epitopes IL4pred il4pred.pl A tool to predict interleukin-4 inducing epitopes AbAg
Third party softwares
Software Status Java Installed SVM_Light Installed Weka Installed R Package Installed HHsuite Installed Modeller Not installed SNNS Installed PERL Installed PHP Installed Galaxy Installed Open-babel with python Installed babel Installed ant Installed CDK Installed MEME/MAST Installed MPIblast Not installed MUMMER Installed SOAPdenovo Installed Velvet Installed CD-HIT Installed RAPIDminer Installed MERCI Installed ChemAxon Not installed Filter-IT Not installed PADEL Installed clustalw/x Installed Blast-old Installed Blast+ Installed MUSCLE Installed Autodock/AutoDock Vina/auto dock tools/auto grid/autodock-CADD/mglutil/ NAMD, PDB2PQR, APBS, MGLToos Installed SPAAN Not installed MAAP Not installed DESMOND Not installed GROMACS Installed ePMV (Blender) Not installed AutoPack Not installed PyMOL Installed JMol Installed RasMol Installed UCSF Chimera Not installed Avogadro Installed LigPlot+ Not installed Scilab Installed MOPAC Installed EMBOSS complete Installed RepeatMasker Not installed PolyPhen Not installed SIFT Not installed GLIMMER Installed UniPro UGENE Installed blast2go Not installed Cytoscape Installed AutoDock Installed CCP4 Not installed Revolution R Installed HMMER Installed DaliLite Not installed Celera Assembler Not installed Newbler Not installed Ray Not installed MIRA Installed PYMOL Installed EMBOSS Suite Installed CMG-biotools Not installed ProSMos Not installed bos Not installed AMOS Not installed SMRT pipeline Not installed IPRSCAN Not installed PROMALS-3D Not installed OrthoMCL Not installed TribeMCL Not installed Samtools Installed IDBA Not installed MOCAT Not installed QIIME Installed PROCAIN Not installed CIRCOS Installed Genome Atlas Not installed FFAS Not installed Biopieces Not installed GAGE Not installed MAKER Not installed GRASS Installed IGV Installed Bowtie Installed tophat Not installed BWA Installed Cufflinks Installed Biopython 1.50 Installed PHYLIP NEW-3.67 Installed Rasmol 220.127.116.11 Installed Readseq 1.7 Installed Vienna RNA 1.8.25 Installed cd-hit Installed cdbfasta Not installed clustalw Installed clustalx Installed hmmer Installed jalview Installed ncbi-blast+ Installed Boxshade Installed Gromacs Installed Garlic Installed Openbabel Installed Chemtool Installed Autodock Installed Autodock-vina Installed BallView Installed ConCavity Installed DSSP Not installed Ghemical Installed PyMol Installed Cain Installed Python-rdkit Installed Raccoon Installed Freediams Installed FreemedForms-Freedata Installed Chemtool Installed OpenClinica Installed Abinit Installed Openmax Installed Ccwatcher Not installed Kalzium Installed Gabedit Installed Gchem3d Not installed Gchemcalc Not installed Gchempaint Installed Genome-chemistry-utils Not installed Molrender Not installed Mopac7 Installed Mpqc Installed Viewmol Installed Xdrawchem Installed PSI3 Installed
In this genomic era, standalone (command-line) bioinformatics tools are helpful for analyzing large-scale data. Therefore, to meet the demand of these standalone tools, in OSDD-Linux we are providing standalone versions of all the methods. It also maintains the privacy of user's data and results. These standalones software are very user-friendly and user can run them by little exposure of linux (It doest not require expertise). By simple execution of program on the terminal (e.g. perl betaturns.pl) will display the usage (e.g. ./betaturns.pl -i /gpsr/examples/example.fasta -o out.betaturns) or help document.Protein Structure Prediction