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.
BLAST is a heuristic algorithm that performs DNA and protein sequence similarity search for common words or k-tuples. PSIPRED
PSIPRED 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. Psiblast
PsiBlast stands for Position-Specific Iterative Blast by NCBI under Blastp suite. HMMER
HMMER is used for searching sequence databases for homologs of protein sequences and for making protein sequence alignment by implementing the Hidden Markov Model. MEME/MAST
MEME/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. ClustalW
ClustalW is a multiple sequence alignment program for DNA and protein provided by EMBL-EBI.
Brief Description SVM
Support Vector Machine are supervised learning models with associated learning algorithm that analyze data and recognize patterns, used for classification and regression analysis.
are models that are capable of machine learning and pattern recognition. Artificial Neural Network kNN
is a non-parametric method for classifying objects based on closest training examples in the feature space. k-nearest neighbor WEKA
is a popular suite of machine learning written in java. Waikato Environment for Knowledge analysis
Brief Description Babel
Babel is a chemical toolbox designed to convert one chemical file format to another. Jmol
Jmol is open source java viewer for chemical structures in 3D. Autodock
Autodock is a suite of automated docking tools designed to predict how drug bind to a receptor of known 3D structure. Dock
Dock uses genetic algorithm to predict the binding modes of small molecules. AutoDock Vina
AutoDock Vina is an open source program for molecular docking on windows platform. PharmaGist
PharmaGist is a freely available webserver that detects the pharmacophore.