Dr. Carlos J. Camacho Laboratory

From Christoph's Personal Wiki
Revision as of 03:47, 4 October 2007 by Christoph (Talk | contribs) (References)

Jump to: navigation, search

The Dr. Carlos J. Camacho Laboratory is where I did scientific research from October 2004 - July 2005, from March 2006 - September 2006 (in absentia), and from December 2006 - February 2007 (in absentia).

Research topics

Results

The research I have done in the laboratory has, so far, yielded two papers published[1][2] and four Web Servers:

Version 1.0: Programmer, Server architect, and administrator; July 2005–December 2006.
Version 2.0: Programmer, Server architect, and administrator; January 2007-present.
Programmer, Server architect, and administrator; January 2005–present (note: This server uses code optimised and run in parallel on 256 processors).
Programmer, Server architect, and administrator; November 2004–present.
Server architect and administrator; September 2004–present.

CAPRI

I was a participant of "Round 6" (17-Jan-2005) and "Round 7" (29-May-2005) of CAPRI. Our group presented the "SmoothDock Server".

Benchmarks

see: Protein-Protein Docking Benchmark

References

  1. Carlos J. Camacho, Ma H, and P. Christoph Champ (2006). Scoring a diverse set of high-quality docked conformations: A metascore based on electrostatic and desolvation interactions. Proteins, 63(4):868-77 DOI:10.1002/prot.20932 . [HubMed]
  2. P. Christoph Champ and Carlos J. Camacho (2007). FastContact: a free energy scoring tool for protein-protein complex structures. Nucleic Acids Research (Web Issue). DOI:10.1093/nar/gkm326 . [HubMed]

Further reading

  • Katchalski-Katzir, E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA. Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natnl Acad Sci USA, 89(6):2195-9.
  • Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D (2003). Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Bio, 331(1):281-99.
  • Proteins: Structure, Function, and Genetics (special edition) Volume 52, Issue 1, 2003, all pages.
  • Bueno M, Camacho CJ, Sancho J (2007). "SIMPLE estimate of the free energy change due to aliphatic mutations: superior predictions based on first principles". Proteins, 68(4):850-62; PMID: 17523191.
  • Bueno M, Camacho CJ (2007). "Acidic groups docked to well defined wetted pockets at the core of the binding interface: A tale of scoring and missing protein interactions in CAPRI". Proteins, [Epub]; PMID: 17803211.

External links