CE-MC: a multiple protein structure alignment server

Abstract

CE-MC server (http://cemc.sdsc.edu) provides a web-based facility for the alignment of multiple protein structures based on C-alpha coordinate distances, using combinatorial extension (CE) and Monte Carlo (MC) optimization methods. Alignments are possible for user-selected PDB (Protein Data Bank) chains as well as for user-uploaded structures or the combination of the two. The whole process of generating multiple structure alignments involves three distinct steps, i.e. all-to-all pairwise alignment using the CE algorithm, iterative global optimization of a multiple alignment using the MC algorithm and formatting MC results using the JOY program. The server can be used to get multiple alignments for up to 25 protein structural chains with the flexibility of uploading multiple coordinate files and performing multiple structure alignment for user-selected PDB chains. For large-scale jobs and local installation of the CE-MC program, users can download the source code and precompiled binaries from the web server.

Figure 1

A screen shot of the CE-MC server main page.

Figure 2

A screen shot of CE-MC results in JOY format, for a subset of structures belonging to the aspartic proteinase family. Uppercase, solvent inaccessible; lowercase, solvent accessible; red, α-helix; blue, β-strand, maroon, 3–10 helix; bold, hydrogen bond to main chain amide; underline, hydrogen bond to main chain carbonyl; cedilla, disulphide bond; italic, positive phi.