Surface & Cavity Analysis
CAVER is a software tool for analysis and visualisation of channels (tunnels) in protein structures. Channels are void pathways leading from a cavity buried in a protein core to the surrounding solvent. Studying of these pathways is highly important for drug design and molecular enzymology.
http://www.caver.cz/
3D-SURFER is web-based software for protein surface comparison and analysis. The server integrates various repertoire of methods to assist in high throughput screening and visualization of protein surface comparisons. It takes less than a second to perform an exhaustive comparison between a single protein surface to all protein structures in the current PDB. Conveniently, the web interface also renders animated protein rotations, displays CATH codes [Orengo CA, Structure, 1997], and structure alignment calculations using the Combinatorial Extension (CE) algorithm [Shindyalov IN and Bourne PE, Protein Eng, 1998]
http://dragon.bio.purdue.edu/3d-surfer/index.php?home
Accurate identification of channels in macromolecules.
http://bioinfo3d.cs.tau.ac.il/MolAxis/
SURF's_UP! is a web tool for analysis of functional relationships in protein families as inferred from protein surface maps comparison. It addresses a situation where only few members of the large homologous family are characterized by experiment and function of others are unknown, either in a general sense or in details (e.g. hydrolase with unknown specificity).
http://asia.genesilico.pl/surfs_up/
Molecular surface of proteins with the electrostatic potential is a representation of protein three dimensional structures, which often gives some clues to infer the function of proteins. eF-surf is a web server to calculate the molecular surface of the up-loaded file with PDB format.
http://ef-site.protein.osaka-u.ac.jp/eF-surf/top.do
Binding sites and active sites of proteins and DNAs are often associated with structural pockets and cavities. castP server uses the weighted Delaunay triangulation and the alpha complex for shape measurements. It provides identification and measurements of surface accessible pockets as well as interior inaccessible cavities, for proteins and other molecules.
http://sts.bioengr.uic.edu/castp/
Protein Interactions Calculator (PIC) is a server which recognizes various kinds of interactions;
http://crick.mbu.iisc.ernet.in/~PIC/
HotPatch finds unusual patches on the surface of proteins, and computes just how unusual they are (patch rareness), and how likely each patch is to be of functional importance (functional confidence (FC).) The statistical analysis is done by comparing your protein's surface against the surfaces of a large set of proteins whose functional sites are known.
http://hotpatch.mbi.ucla.edu/
MolLoc takes in input two molecules and superimposes them on their two most extended similar regions. This server can be used to test if two molecules with different sequences and folds share any local surface similarity.
http://bcb.dei.unipd.it/MolLoc/
No comments:
Post a Comment