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