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The Burnham Institute
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Bioinformatics Server |
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FFAS03 |
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A new, updated and maintained version of the Fold & Function Assignment System (FFAS).
The FFAS fold assignment method is based on the profile-profile matching algorithm.
The crucial part
of the algorithm is the novel, two dimensional weighting scheme which takes into account
the topology of the evolutionary tree of all the proteins in the homologous family.
User registration required. This service is not available to commercial users.
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FATCAT |
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Pairwise flexible protein structure alignment server. See Bioinformatics, 2003, 19(Suppl 2):II246-II255 for details.
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POSA |
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Multiple flexible protein structure alignment server. See Bioinformatics, 2005 21(10):2362-2369
for details
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TOPS++FATCAT |
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TOPS++FATCAT uses TOPS to limit the search space of the aligned fragment pairs (AFPs)
in the flexible alignment of protein structures performed by the FATCAT algorithm.
Such intuitions could help speed up similarity searches and make it easier to understand the results of such analyses.
See
BMC Bioinformatics, 9:358, 2008. for details.
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XtalPred |
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XtalPred server is a server to predict protein crystallizability. Please see Bioinformatics, 2007 23(24):3403-5 for server information and see Protein Science, 2007 16(11):2472-82 for method details.
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JAFA |
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JAFA provides clear, concise annotation to protein sequences.
The Joined Assembly of Function Annotations, a function
annotation meta-server, accepts a protein sequence, and queries several
function prediction programs. The programs' results are assembled and
reported as Gene Ontology
terms, with links to the original predictions, a graphic description,
and XML files so that JAFA can be incorporated into your own work-flow.
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CADO |
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Comparative Analysis of protein Domain Organization. A graph theory method to survey and compare domain organization across genomes. Described in Genome Research, 2004, 14:343-353
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Fragnostic |
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Mapping the Protein Structure Universe using Recurring Structural Fragments. A graph theory method to survey inter-fold similarities. Described in an upcoming manuscript in Journal of Molecular Biology
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SEA |
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A novel approach to protein sequence alignment, the structure SEgment Alignment (SEA) is based on the network mathcing approach, and profile-profile comparison of short fragments of sequence. See Bioinformatics, 2003, 19:742-9 for details.
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FRAGlib |
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This server predicts local structure segments in proteins by the profile-profile matching algorithm
based on the database of short (7-19aa) secondary structural motifs chosen from ASTRAL SCOP database.
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Pacgum |
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Pacgum is a tool for checking the regularity of atomic packing in any
given 3D model of protein.
It discriminates low-resolution from high-resolution
protein structures and uses a purely geometric
approach which is independent
from the origin of the model.
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Wikiomics |
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Wikiomics is a wiki for the bioinformatics community that is hosted on
one of our servers. The principle is to reduce the communication barriers
between scientists, by letting anyone instantly edit, review, update and
discuss any part of the web site. Hosted under an independent domain name,
we are confident Wikiomics will become a tool of choice for every modern
scientist concerned with bioinformatics.
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