Required packages in OSDDlinux

Twenty-first century biological science has transformed into data-intensive sciences because various scientific breakthroughs will be powered by advanced computing capabilities which help researchers to manipulate and explore huge datasets. So computational biological techniques will be useful to organize and interpret plentitude of biological data. This page contains brief description of commonly used computational packages required in OSDDlinux.

Prerequisite software for OSDDlinux

BLASTBLAST is a heuristic algorithm that performs DNA and protein sequence similarity search for common words or k-tuples.
PSIPREDPSIPRED is a protein secondary structure prediction program that includes two feed-forward neural networks to perform an analysis of results obtained by the PSI-BLAST.
PsiblastPsiBlast stands for Position-Specific Iterative Blast by NCBI under Blastp suite.
HMMERHMMER is used for searching sequence databases for homologs of protein sequences and for making protein sequence alignment by implementing the Hidden Markov Model.
MEME/MASTMEME/MAST is a motif based sequence analysis tool that allows to discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences.
ClustalWClustalW is a multiple sequence alignment program for DNA and protein provided by EMBL-EBI.

Machine learning tools used in OSDDlinux

Package NameBrief Description
SVMSupport Vector Machine are supervised learning models with associated learning algorithm that analyze data and recognize patterns, used for classification and regression analysis.
ANNArtificial Neural Network are models that are capable of machine learning and pattern recognition.
kNNk-nearest neighbor is a non-parametric method for classifying objects based on closest training examples in the feature space.
WEKAWaikato Environment for Knowledge analysis is a popular suite of machine learning written in java.

Chemoinformatics packages in OSDDlinux

Package NameBrief Description
BabelBabel is a chemical toolbox designed to convert one chemical file format to another.
JmolJmol is open source java viewer for chemical structures in 3D.
AutodockAutodock is a suite of automated docking tools designed to predict how drug bind to a receptor of known 3D structure.
DockDock uses genetic algorithm to predict the binding modes of small molecules.
AutoDock VinaAutoDock Vina is an open source program for molecular docking on windows platform.
PharmaGistPharmaGist is a freely available webserver that detects the pharmacophore.