Bioinformatics Tools

Primary Structure Analysis

ProtPram : Calculate physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, pI, extinction coefficient, etc.) (ExPASy)

The Sequence Manipulation Suite: A collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences

Sequence Similarity

Pairwise BLAST : (Similarity Search between Two Sequences)
BLAST : Sequence Database Search Tool (NCBI)
FASTA : Protein Sequence Database Search Tool (NPSA)

Multiple Sequence Alignment

Clustal W : at European Bioinformatics Institute, EMBL
Clustal W – Proteins : at Network Protein Sequence Analysis
Clustal W – DNA : at NPSA

Phylogenetic Tree Construction

Phylip programs

Structural Alignment

DALI : Structural Similarity Tool
FSSP : Fold classification based on Structure alignment of Proteins

Secondary Structure Prediction

PredictProtein – Secondary Structure Prediction Tool
PHD : PHD Secondary Structure Prediction Method at NPSA
SOPMA : SOPMA Secondary Structure Prediction at NPSA

Advanced Primary Structure Analysis

ExPASy : Proteomics Tools
EMBL-European Bioinformatics Institute
Pfam : Protein families database of Alignments and HMMs (Sanger)
PatScan : Scan Sequence Database for Patterns
PattinProt : Pattern Search at NPSA
Profile Scan : Motif Search in a Protein Sequence
Scan Prosite : Search Protein Sequence for Profiles at Prosite
SMART : Simple Modular Architechture Research Tool at EMBL

Homology Modeling

Swiss-Model : Homology Modeling Tool

Other Useful Links

Spectroscopy Resource
GENSCAN
: Protein Prediction Tool
Multicoil : Predicts location of coiled-coilregions in protein sequence
BCM-HGSC : Human Genome Sequencing Center, Baylor College
DOE-MBI : Useful Resource at the Structural Biology Lab, UCLA