The Bioperl Project
international association of developers of open source Perl tools for
bioinformatics, genomics and life science research.
The BioJava Project
is an open-source
project dedicated to providing Java tools for processing biological data.
This will include objects for manipulating sequences, file parsers, CORBA
interoperability, access to ACeDB, dynamic programming, and simple
(Basic Local Alignment Search Tool) is a set of similarity search
programs designed to explore all of the available sequence databases
regardless of whether the query is protein or DNA. The BLAST programs have
been designed for speed, with a minimal sacrifice of sensitivity to
distant sequence relationships.
computer-aided chemistry modeling package for experimental chemists
Clustal W - a
common purpose multiple sequence alignment program for DNA or proteins.
Chimera - UCSF
Chimera is a highly extensible, interactive molecular graphics program.
FASTA3 - Sequence
similarity and homology searching against nucleotide and protein database
using Fasta3. Please note that this service will be phased out shortly. Use the new version above.
Proteomes and Genomes
FASTA - This tool uses the Fasta programs to provide sequence
similarity and homology searching against complete proteome or genome
based on Structure-Structure alignment of Proteins - The
FSSP database is based on exhaustive all-against-all 3D structure
comparison of protein structures currently in the Protein Data Bank (PDB).
The classification and alignments are automatically maintained and
continuously updated using the
Dali search engine.
Gaussian - Starting from the
basic laws of quantum mechanics, Gaussian predicts the energies,
molecular structures, and vibrational frequencies of molecular systems,
along with numerous molecular properties derived from these basic
computation types. (also
- GOLD is a program for calculating the docking modes of small molecules
into protein binding sites. (Also includes SILVER for
Post-processing of Docking Results.)
Gromacs - "The Worlds Fastest
Molecular Dynamics." Howto create inputs for gromacs simulations -
PowerPoint , PDF
allows you to query your protein sequence against InterPro.
MaxSprout is a fast database algorithm for generating protein backbone and
side chain co-ordinates from a C(alpha) trace.
MOE - ChemComp MOE is a comprehensive
software system addressing the needs of today's research disciplines
including Bioinformatics, Cheminformatics, Protein Modeling,
Structure-Based Design, High Throughput Discovery and Molecular Modeling
NAMD - Scalable
Molecular Dynamics, NAMD is a parallel molecular dynamics code designed
for high-performance simulation of large biomolecular systems
Protein Explorer -
for looking at macromolecular structure and its relation to function (this
software is the newest version of RASMOL).
Swiss Pdb-Viewer - Swiss-PdbViewer
is an application that provides a user friendly interface allowing to
analyze several proteins at the same time. The proteins can be
superimposed in order to deduce structural alignments and compare their
active sites or any other relevant parts. Amino acid mutations, H-bonds,
angles and distances between atoms are easy to obtain thanks to the
intuitive graphic and menu interface.
Classifications of Proteins (SCOP) - Nearly all proteins have
structural similarities with other proteins and, in some of these cases,
share a common evolutionary origin. The
database, created by manual inspection and abetted by a battery of
automated methods, aims to provide a detailed and comprehensive
description of the structural and evolutionary relationships between all
proteins whose structure is known. As such, it provides a broad survey of
all known protein folds, detailed information about the close relatives of
any particular protein, and a framework for future research and
VMD - Visual
Molecular Dynamics (VMD) is a molecular visualization program for
displaying, animating, and analyzing large biomolecular systems using
3-D graphics and built-in scripting.
is a suite of programs designed to modify and check the validity of pdb
entries. The underlying premise is to make a change to the given structure
and test what happens. WhatIf allows homology modeling, docking
calculations, placement and optimization of hydrogen bonds, and structure
validation. (Site license information is found at
WU Blast - Washington University
WU Blast2 -
Tool Version 2.0