:: 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
Swelfe is a program that enables you to find internal repeats in DNA sequences, amino-acid sequences or 3D structures.
::DEVELOPER
RPBS(Ressource Parisienne en BioInformatique Structurale)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Anne-Laure Abraham; Eduardo P. C. Rocha; Joel Pothier
Swelfe : a detector of internal repeats in sequences and structures
Bioinformatics 2008; doi: 10.1093/bioinformatics/btn234
:: DESCRIPTION
ROADTRIPS is a C program that performs single-SNP, case-control association testing in samples with partially or completely unknown population and pedigree structure.ROADTRIPS uses an empirical covariance matrix calculated from genomewide SNP data to correct for unknown population and pedigree structure, while maintaining high power by taking advantage of known pedigree information when it is available. The program is applicable to association studies with completely general combinations of related and unrelated individuals. Analysis can be performed genomewide (currently just for autosomes).
::DEVELOPER
Timothy Thornton and Mary Sara McPeek
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Thornton T., McPeek M. S.
“ROADTRIPS: Case-Control Association Testing with Partially or Completely Unknown Population and Pedigree Structure” (2010)
American Journal of Human Genetics, vol 86, pp. 172-184.
:: DESCRIPTION
ALISS (Alignment of Structures and Sequences) is a tool for structure-structure, sequence-structure and sequence-sequence alignment.
::DEVELOPER
The Centre for Integrative Bioinformatics VU
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kleinjung, J., Romein, J., Lin, K. and Heringa, J. (2004)
Contact-based sequence alignment,
Nucleic Acids Research 32(8), 2464-2473.
:: DESCRIPTION
Sequoia (sequence and structure alignment) is a command-line tool for the alignment of molecular protein sequences and atomic structures. It is not exactly simulation, but it needs a stable home. I wrote it over the past 10 years, and some users have started to complain that my home server is no longer reliably available.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
covarionTest is a perl script that performs the heterogeneity or the covarion test.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Cecile Ane, J. Gordon Burleigh, Michelle M. McMahon, Michael J. Sanderson.
Covarion structure in the plastid genome evolution: a new statistical test.
Mol. Biol Evol., 22(4):914-924. 2005
:: DESCRIPTION
WinDrawChem is a freeware two-dimensional molecule drawing program for Windows. It is similar in functionality to other molecule drawing programs such as ChemDraw (TM, CambridgeSoft). It can read and write MDL Molfiles to allow sharing between XDrawChem and other chemistry applications, as well as read ChemDraw binary and text files.
::DEVELOPER
Bryan Herger , bherger@users.sourceforge.net
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
WinDrawChem is distributed under the terms of the GNU General Public License. There is also additional copyright information. These files are also included in the distribution.
:: DESCRIPTION
SCALI (Structural Core ALIgnment), can efficiently find conserved packing arrangements, even if they are non-sequentially ordered in space. SCALI alignments conserve remote sequence similarity and contain fewer alignment errors. Clustering of our pairwise non-sequential alignments shows that recurrent packing arrangements exist in topologically different structures. For example, the 3-layer sandwich domain architecture may be divided into four structural subclasses based on internal packing arrangements. These subclasses represent an intermediate level of structure classification, more general than topology but more specific than architecture as defined in CATH. A strategy is presented for developing a set of predictive hidden Markov models based on multiple SCALI alignments.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citaiton
Yuan X & Bystroff, C. (2005)
Non-sequential Structure-based Alignments Reveal Topology-independent Core Packing Arrangements in Proteins.
Bioinformatics 27(7):1010-1019.
:: DESCRIPTION
Friend (Integrated FRont-END) is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities such as: structure visualization with different rendering and coloring, sequence alignment, and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including: structure alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions, and protein super-families.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Friend, an integrated analytical front-end application for bioinformatics. Bioinformatics. 2005 Sep 15(18):3677-8.
:: DESCRIPTION
SPICE is a browser for protein sequences, structures and their annotations. It can display annotations for PDB, UniProt and Ensembl Peptides. All data is retrieved from different sites on the Internet, that make their annotations available using the DAS protocol. It is possible to add new annotations to SPICE, and to compare them with the already available information.
::DEVELOPER
Andreas Prlic, Thomas Down, Tim Hubbard.
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Adding some SPICE to DAS
Bioinformatics Volume 21, suppl_2 Pp. ii40-ii41
Andreas Prlic, Thomas A. Down and Tim J. P. Hubbard
