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EMBOSS |
WEB |
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EMBOSS is a free Open Source software analysis package specially
developed for the needs of the molecular biology (e.g. EMBnet)
user community. The software automatically copes with data in a
variety of formats and even allows transparent retrieval of
sequence data from the web. Also, as extensive libraries are
provided with the package, it is a platform to allow other
scientists to develop and release software in true open source
spirit.
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HOME:
http://emboss.sourceforge.net/ |
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Ligand.Info |
WEB |
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Ligand.Info is a compilation of various publicly available
databases of small molecules such as
ChemBank,
ChemPDB,
KEGG,
NCI,
AKos GmbH,
Asinex Ltd, and
TimTec.
The total size of the Meta-Database is 1 million entries. The
compound records contain calculated three-dimensional
coordinates and sometimes information about biological activity.
Some molecules have information about FDA drug approving status
or about anti-HIV activity. Meta-Database can be downloaded in SDF format and used for virtual high-throughput screening of new
potential drugs. The database can also be screened using a
Java-based tool.
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HOME:
http://ligand.info/ |
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PDB |
FTP
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WEB |
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Archive of experimentally-determined, biological macromolecule
3-D structures from the Brookhaven National Laboratory.
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HOME:
http://www.rcsb.org/pdb/ |
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phpMyAdmin |
WEB |
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phpMyAdmin is a tool written in PHP intended to handle the
administration of MySQL over the web.
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HOME:
http://www.phpmyadmin.net/home_page/ |
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PredictProtein |
WEB |
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PredictProtein is
a service for sequence analysis, and structure prediction.
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HOME:
http://www.embl-heidelberg.de/predictprotein/predictprotein.html |
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SCOP |
WEB |
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The
SCOP
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 classification.
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HOME:
http://scop.mrc-lmb.cam.ac.uk/scop/ |
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Sequence
Manipulation Suite 2 |
WEB |
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The Sequence
Manipulation Suite is a collection of JavaScript programs for
generating, formatting, and analyzing short DNA and protein
sequences. It is commonly used by molecular biologists, for
teaching purposes, and for program and algorithm testing.
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HOME:
http://bioinformatics.org/sms2/ |
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WEBLOGO |
WEB |
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Sequence logos
are a graphical representation of an amino acid or nucleic acid
multiple sequence alignment developed by Tom Schneider and Mike
Stephens. Each logo consists of stacks of symbols, one stack for
each position in the sequence. The overall height of the stack
indicates the sequence conservation at that position, while the
height of symbols within the stack indicates the relative
frequency of each amino or nucleic acid at that position. In
general, a sequence logo provides a richer and more precise
description of, for example, a binding site, than would a
consensus sequence.
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HOME:
http://weblogo.berkeley.edu/ |
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