CE-MC: A multiple protein structure alignment server

Chittibabu Guda, Sifang Lu, Eric D. Scheeff, Philip E. Bourne, Ilya N. Shindyalov

Research output: Contribution to journalArticlepeer-review

98 Scopus citations


CE-MC server (http://cemc.sdsc.edu) provides a web-based facility for the alignment of multiple protein structures based on C-α 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.

Original languageEnglish (US)
Pages (from-to)W100-W103
JournalNucleic acids research
Issue numberWEB SERVER ISS.
StatePublished - Jul 1 2004
Externally publishedYes

ASJC Scopus subject areas

  • Genetics


Dive into the research topics of 'CE-MC: A multiple protein structure alignment server'. Together they form a unique fingerprint.

Cite this