:: DESCRIPTION
urms (unit-vector root mean squared) is a protein structure comparison program that compares two structures (in PDB format).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Golan Yona and Klara Kedem. (2005).
The URMS-RMS hybrid algorithm for fast and sensitive local protein structure alignment.
Journal of Computational Biology 12 12-32.
:: DESCRIPTION
prof_sim is a profile-profile comparison program that compares PSI-BLAST profiles.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Golan Yona and Michael Levitt.
Within the twilight zone: A sensitive profile-profile comparison tool based on information theory. (2002).
Journal of Molecular Biology 315 1257-1275.
:: DESCRIPTION
COMPASS runs a search with submitted alignment (or sequence) as a query against a database of protein families.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
R.I. Sadreyev, M. Tang, B. Kim and N.V. Grishin (2009)
COMPASS server for homology detection: improved statistical accuracy, speed, and functionality.
Nucleic Acids Res doi:10.1093/nar/gkp360.
:: DESCRIPTION
MS_Align is a soft ware of comparison of minisatellites.
::DEVELOPER
Bérard S, Rivals E.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
“Comparison of minisatellites.”
Bérard S., Rivals E.
Journal of Computational Biology. 2003 10(3-4):357-72.
:: DESCRIPTION
RNACluster is an integrated computational software which implements 6 common structure distances to measure the (dis)similarity of RNA secondary structures including base pair distance, mountain distance, morphological distance, tree edit distance, string edit distance and our in-house structure matrix distance, and one effective cluster approach for the ensemble clustering using a minimum spanning tree (MST) based algorithm. RNACluster can be used to study the characteristics of RNA secondary structures, RNA structure conformational switches, RNA conformational energy landscapes and RNA secondary structure prediction based on the clustering of structure ensemble.
::DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Liu Q, Olman V, Liu H, Ye X, Qiu S, Xu Y.
RNACluster: An integrated tool for RNA secondary structure comparison and clustering.
J Comput Chem. 2008 Jul 15;29(9):1517-26.
:: DESCRIPTION
MUTPROF is a Monte-Carlo-Markov-Chain implementation of the hypergeometric test for sparse 3-dimensional contingency tables (in the spirit of Fisher’s exact test). It allows the comparison of up to 200 positions within the same gene, but between different tissues and/or species.
MUTCOMP serves to compare two nucleotide substitution matrices for one or more, possibly different genes, tissues or species, taking the expected mutation frequencies into account.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
GSC is a tcl/tk program which makes it easy to analyze chemical shifts of selected atoms between chemical shift files
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Wolfram Gronwald , R. Boyko, and B.D. Sykes.
GSC: a graphical program for NMR chemical shifts comparison
Comput Appl Biosci (1997) 13 (5): 557-558
:: DESCRIPTION
STRuster is a method for clustering alternative structural models corresponding to different structure determination experiments. Alternative structural models, determined by X-ray crystallography or NMR spectroscopy, are frequently available for a given protein. These models can present significant structural dissimilarity. The structures are classified according to backbone structure similarity.
::DEVELOPER
Francisco S. Domingues , Max-Planck-Institut Informatik
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Domingues, F. S.; Rahnenfuhrer, J.; Lengauer, T.,
Conformational analysis of alternative protein structures.
Bioinformatics 2007, 23 (23), 3131-8.
:: DESCRIPTION
CLICK is capable of superimposing the 3D structures of biomolecules, the Cartesian coordinates of whose constituent atoms are presented in the PDB format. In addition to coordinates, the web server can make use of similarity of other structural features such as secondary structure, solvent accessible surface area, and residue depth to guide the alignment. CLICK first looks for cliques of points (3–7 residues) that are structurally similar in the pair of structures to be aligned. Using these local similarities, a one-to-one equivalence is charted between the residues of the two structures. A least square fit then superimposes the two structures. Our method is especially powerful in establishing protein relationships by detecting similarities in structural subdomains, domains and topological variants.
::DEVELOPER
Bioinformatics Institute of Singapore.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Nguyen,M.N., Tan,K.P., and Madhusudhan,M.S. (2011)
CLICK – Topology independent comparison of biomolecular 3D structures.
Nucleic Acids Res., doi:10.1093/nar/gkr393
:: DESCRIPTION
CMap (omparative Map Viewer) is a web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. A user can compare an unlimited number of maps, view pair-wise comparisons of known correspondences, and search for maps or for features by name, species, type and accession. CMap is freely available, can run on a variety of database engines and uses only free and open software components.
::DEVELOPER
the Generic Model Organism Database
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ken Youens-Clark, Ben Faga, Immanuel V. Yap, Lincoln Stein and Doreen Ware
CMap 1.01: a comparative mapping application for the Internet.
, Bioinformatics 2009 25(22):3040-3042; doi:10.1093/bioinformatics/btp458.
