A multipurpose high performance production molecular simulator MG-RAST - Home about [CP2K Open Source Molecular Dynamics ] PathVisio - pathway drawing and pathway analysis tool emergent Ascalaph Designer - molecular dynamics in graphic environment Molecular models and dynamic simulations Ascalaph Designer is a general-purpose program for molecular dynamic simulations. Under a single graphical environment are represented as their own implementation of molecular dynamics as well as the methods of classical and quantum mechanics of popular programs. Features: Documentation Download Download from SourceForge
Coot Is this the "Official Home of Coot on the Web™"? Yes - welcome. What does Coot stand for? Crystallographic Object-Oriented Toolkit What does it do? Coot is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data. Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots, skeletonization, non-crystallographic symmetry and more. What's the latest stable release? What's it like? Coot has some features that resemble those of Frodo, O, Quanta and XtalView's XFit. Coot is under development. Is there a Coot FAQ? Yes. Is there a Coot Mailing list? There is a Coot email list now hosted by the jiscmail service : Is there Coot documentation? Yes.... The 2012 ACA Coot Basics can be found here. The 2012 ACA Coot Extras can be found here. Yep.
YASS : genomic similarity search tool What is YASS YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments). Like most of the heuristic pairwise local alignment tools for DNA sequences (FASTA, BLAST, PATTERNHUNTER, BLASTZ/LASTZ, LAST ...), YASS uses seeds to detect potential similarity regions, and then tries to extend them to local alignments. This genomic search tool uses multiple transition constrained spaced seeds that enable to search more fuzzy repeats, as non-coding DNA/RNA. Another simple, but interesting feature is that you can specify the seed pattern used in the search step (as provided for example by iedera). Main features of YASS are: YASS produces the common blast tabular output files ("-d 3" option). If you use this program in your work, please cite : [1] L. Of course, your comments and suggestions are welcome and always appreciated! Query YASS Online You can query YASS from this server: yass.php. Papers/Links that use/cite YASS