Biomedical subjects

S S Sheik

Publications and source records attributed to S S Sheik.

5 recordsLinked to original sources

PubMed2003

SEM (Symmetry Equivalent Molecules): A web-based GUI to generate and visualize the macromolecules.

SEM, Symmetry Equivalent Molecules, is a web-based graphical user interface to generate and visualize the symmetry equivalent molecules (proteins and nucleic acids). In addition, the program allows the users to save the three-dimensional atomic coordinates of the symmetry equivalent molecules in the local machine. The widely recognized graphics program RasMol has been deployed to visualize the reference (input atomic coordinates) and the symmetry equivalent molecules. This program is written using CGI/Perl scripts and has been interfaced with all the three-dimensional structures (solved using X-ray crystallography) available in the Protein Data Bank. The program, SEM, can be accessed over the World Wide Web interface at http://dicsoft2.physics.iisc.ernet.in/sem/ or http://144.16.71.11/sem/.

Computer Graphics↗

PubMed2003

CAP: conformation angles package-displaying the conformation angles of side chains in proteins.

SUMMARY: A graphics package has been developed to display all side chain conformation angles of the user selected residue in a given protein structure. The proposed package is incorporated with all the protein structures (solved using X-ray diffraction and NMR spectroscopy) available in the Protein Data Bank. The package displays the multiple conformations adopted by a single amino acid residue whose structure is solved and refined at very high resolution. In addition, it shows the percentage distribution of the side chain conformation angles in different rotameric states. AVAILABILITY: http://144.16.71.146/cap/

Amino Acids↗

PubMed2003

CADB: Conformation Angles DataBase of proteins.

Conformation Angles DataBase (CADB) provides an online resource to access data on conformation angles (both main-chain and side-chain) of protein structures in two data sets corresponding to 25% and 90% sequence identity between any two proteins, available in the Protein Data Bank. In addition, the database contains the necessary crystallographic parameters. The package has several flexible options and display facilities to visualize the main-chain and side-chain conformation angles for a particular amino acid residue. The package can also be used to study the interrelationship between the main-chain and side-chain conformation angles. A web based JAVA graphics interface has been deployed to display the user interested information on the client machine. The database is being updated at regular intervals and can be accessed over the World Wide Web interface at the following URL: http://144.16.71.148/cadb/.

Animals↗

PubMed2002

PDB Goodies--a web-based GUI to manipulate the Protein Data Bank file.

PDB Goodies is a web-based graphical user interface (GUI) to manipulate the Protein Data Bank file containing the three-dimensional atomic coordinates of protein structures. The program also allows users to save the manipulated three-dimensional atomic coordinate file on their local client system. These fragments are used in various stages of structure elucidation and analysis. This software is incorporated with all the three-dimensional protein structures available in the Protein Data Bank, which presently holds approximately 18 000 structures. In addition, this program works on a three-dimensional atomic coordinate file (Protein Data Bank format) uploaded from the client machine. The program is written using CGI/PERL scripts and is platform independent. The program PDB Goodies can be accessed over the World Wide Web at http://144.16.71.11/pdbgoodies/.

Computer Graphics↗

PubMed2002

Ramachandran plot on the web.

A graphics package has been developed to display the main chain torsion angles phi, psi (phi, Psi); (Ramachandran angles) in a protein of known structure. In addition, the package calculates the Ramachandran angles at the central residue in the stretch of three amino acids having specified the flanking residue types. The package displays the Ramachandran angles along with a detailed analysis output. This software is incorporated with all the protein structures available in the Protein Databank.

Amino Acid Motifs↗