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.

Protein Structure Prediction
Name of standalonemain programApplications
APSSP2apssp2.plAdvanced Protein Secondary Structure Prediction Server
PROCLASSproclass.plPrediction of Protein Structure Classification
PSAAnalysis of Protein Sequence and Multiple Alignment
BetatPred2betatpred2.plPrediction of betaturns in proteins
CHpredictchpredict.plPrediction of CH..O and CH..Pi interactions
AR_NHPredar_nhpred.plPrediction of aromatic backbone NH interaction in proteins
TBBPredtbbpred.plPrediction of Transmembrane Beta Barrel in Proteins
BetaTurnsbetaturns.plPrediction of betaturn types in protein
BhairPredbhairpred.plPrediction of Beta Hairpins
GammaPredgammapred.plPrediction of Gamma turns in protein
AlphaPredalphapred.plPrediction of Alpha turns in protein
PepStrpepstr.pl3D structure prediction of bioactive peptides
SarPredsarpred.plA neural network based method predicts the real value of surface acessibility (SA) by using multiple sequence alignment
FiSipredfisipred.plPrediction of backbone torsion angles phi and psi

Epitope based Vaccines


PROPRED1propred1.plprediction of promiscuous MHC Class-I binding sites
nHLA4prednhlapred.plA neural network based MHC Class-I Binding Peptide Prediction Server
MMBpredPrediction of mutated high affinity and promiscuous MHC class-I binding peptides from protein sequence
Pcleavagepcleavage.plAn SVM based method for proteosome cleavage prediction
TAPpredtappred.plTAPPred is a tool for predicting binding affinity of peptides toward the TAP transporter
CTLpredctlpred.pl CTLpred: Prediction of cytotoxic T cell epitopes
PROPREDpropred.plPrediction of HLA-DR binding sites
HLADR4predhladr4pred.plSVM based method for predicting HLA-DRB1 binding peptides in an antigen sequence
CBtopeConformational B-cell epitope prediction
LBtopePrediction of linear B-cell epitopes
MHC2predSVM based method for prediction of promiscuous MHC class II binding peptides
MHCmhc.plMatrix Optimization Technique for Predicting MHC binding Core
MHCbenchmhcbench.plEvaluation of Major Histocompatibility Complex (MHC) binding peptide prediction algorithms
BCEpredbcepred.plBcepred: Prediction of linear B-cell epitopes, using physico-chemical properties
ABCpredabcpred.plPrediction of B-cell epitopes in antigen sequence
HLApred
HLA_affi
FDR4Prediction of binding affinity of peptide binders in an antigenic sequence for a MHC class II allele HLA-DRB1*0401
TmhcpredPrediction of MHC Class I and II binding peptides
IFNepitopeifnepitope.plA server for predicting and designing interferon-gamma inducing epitopes
IL4predil4pred.plA tool to predict interleukin-4 inducing epitopes
AbAg

Third party softwares
SoftwareStatus
JavaInstalled
SVM_LightInstalled
WekaInstalled
R PackageInstalled
HHsuiteInstalled
ModellerNot installed
SNNSInstalled
PERLInstalled
PHPInstalled
GalaxyInstalled
Open-babel with pythonInstalled
babelInstalled
antInstalled
CDKInstalled
MEME/MASTInstalled
MPIblastNot installed
MUMMERInstalled
SOAPdenovoInstalled
VelvetInstalled
CD-HITInstalled
RAPIDminerInstalled
MERCIInstalled
ChemAxonNot installed
Filter-ITNot installed
PADELInstalled
clustalw/xInstalled
Blast-oldInstalled
Blast+Installed
MUSCLEInstalled
Autodock/AutoDock Vina/auto dock tools/auto grid/autodock-CADD/mglutil/ NAMD, PDB2PQR, APBS, MGLToosInstalled
SPAANNot installed
MAAPNot installed
DESMONDNot installed
GROMACSInstalled
ePMV (Blender)Not installed
AutoPackNot installed
PyMOLInstalled
JMolInstalled
RasMolInstalled
UCSF ChimeraNot installed
AvogadroInstalled
LigPlot+Not installed
ScilabInstalled
MOPACInstalled
EMBOSS completeInstalled
RepeatMaskerNot installed
PolyPhenNot installed
SIFTNot installed
GLIMMERInstalled
UniPro UGENEInstalled
blast2goNot installed
CytoscapeInstalled
AutoDockInstalled
CCP4Not installed
Revolution RInstalled
HMMERInstalled
DaliLiteNot installed
Celera AssemblerNot installed
NewblerNot installed
RayNot installed
MIRAInstalled
PYMOLInstalled
EMBOSS SuiteInstalled
CMG-biotoolsNot installed
ProSMosNot installed
bosNot installed
AMOSNot installed
SMRT pipelineNot installed
IPRSCANNot installed
PROMALS-3DNot installed
OrthoMCLNot installed
TribeMCLNot installed
SamtoolsInstalled
IDBANot installed
MOCATNot installed
QIIMEInstalled
PROCAINNot installed
CIRCOSInstalled
Genome AtlasNot installed
FFASNot installed
BiopiecesNot installed
GAGENot installed
MAKERNot installed
GRASSInstalled
IGVInstalled
BowtieInstalled
tophatNot installed
BWAInstalled
CufflinksInstalled
Biopython 1.50Installed
PHYLIP NEW-3.67Installed
Rasmol 2.7.3.1Installed
Readseq 1.7Installed
Vienna RNA 1.8.25Installed
cd-hitInstalled
cdbfastaNot installed
clustalwInstalled
clustalxInstalled
hmmerInstalled
jalviewInstalled
ncbi-blast+Installed
BoxshadeInstalled
GromacsInstalled
GarlicInstalled
OpenbabelInstalled
ChemtoolInstalled
AutodockInstalled
Autodock-vinaInstalled
BallViewInstalled
ConCavityInstalled
DSSPNot installed
GhemicalInstalled
PyMolInstalled
CainInstalled
Python-rdkitInstalled
RaccoonInstalled
FreediamsInstalled
FreemedForms-FreedataInstalled
ChemtoolInstalled
OpenClinicaInstalled
AbinitInstalled
OpenmaxInstalled
CcwatcherNot installed
KalziumInstalled
GabeditInstalled
Gchem3dNot installed
GchemcalcNot installed
GchempaintInstalled
Genome-chemistry-utilsNot installed
MolrenderNot installed
Mopac7Installed
MpqcInstalled
ViewmolInstalled
XdrawchemInstalled
PSI3Installed