Marchler-Bauer A, Anderson JB, Derbyshire MK, DeWeese-Scott C, Gonzales NR, Gwadz M, Hao L, He S, Hurwitz DI, Jackson JD, Ke Z, Krylov D, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Thanki N, Yamashita RA, Yin JJ, Zhang D, Bryant SH. CDD: a conserved domain database for interactive domain family analysis.
Nucleic Acids Res. 2007;35 (Database Issue):D237-40.
Se-Al is an application for creating multiple sequence alignments from nucleotide and amino acid sequences. At the moment it does not do any automatic alignments but is intended for the production of hand alignments and for preparing input for alignment programs such as CLUSTAL and phylogeny reconstruction programs such as PHYLIP and PAUP. It is particularly useful for manipulating protein coding DNA/RNA sequences.
NDE (NEXUS Data Editor) is a program to create and edit NEXUS format data files on computers running Microsoft Windows 95/NT 4.0. The main motivation behind my writing the program was to provide an easy to use data editor similar to that provided in the Macintosh program MacClade (note that NDE has none of the data or tree analysis features of MacClade). The NEXUS format is becoming more widely used on PCs now that DOS and Windows versions of PAUP* are available for testing.
PDB Editor (Protein Data Bank ,PDB, File Editor) is a tool for protein crystallographers to expedite selective edit / data extraction / analysis of their PDB files. It allows the user to selectively search, select, extract and edit information in parallel.
StrukEd is not only an editor for molecules that allows the input of chemical structures in a very comfortable way. Additionally, StrukEd can import the results of a variety of quantum-chemical methods and can visualize these results at a sophisticated level.
The Input of Molecules is supported by extensive fragment and functional groups libraries; these can easily be changed and extended on user’s demand. StrukEd checks the created structures in terms of their chemical plausibility, thus providing help for the user in order to avoid errors.
The program generates a 3D model starting from the valence bond input. According to its quality, this model can be used to visualize bond lengths, angles and torsion angles of the three-dimensional structure as well as an input for other optimization programs.
MCDL (Modular Chemical Descriptor Language) is a small Java molecular viewer/editor for chemical structures, stored in Modular Chemical Descriptor Language linear notation. The editor supports the MCDL format, in which structures are presented in compact canonical form and is capable of restoring bond orders as well as of managing atom and bond drawing overlap. A small database of cage and large cyclic fragment is used for optimal representation of difficult-to-draw molecules. The improved algorithm of the structure diagram generation can be used for other chemical notations that lack atomic coordinates (SMILES, InChI).
::DEVELOPER
Sergei Trepalin (Institute of Physiologically Active Compounds RAS)