Difference between revisions of "Dr. Carlos J. Camacho Laboratory"

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== Benchmarks ==
 
== Benchmarks ==
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A benchmark of 84 protein-protein interactions with known complexed structures has been developed for testing docking methods<ref name=Minteris>Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z (2005). Protein-Protein Docking Benchmark 2.0: an Update. ''Proteins, 60(2):214-6''.</ref>. The set is chosen to cover a wide range of interaction types, and to avoid repeated features, such as the profile of interactors' structural families according to the [http://scop.mrc-lmb.cam.ac.uk/scop/ SCOP] database. Benchmark elements are classified into three levels of difficulty (the most difficult containing the largest change in backbone conformation). The protein-protein docking benchmark contains examples of enzyme-inhibitor, antigen-antibody and homomultimeric complexes.
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see: [[Protein-Protein Docking Benchmark]]
  
 
== References ==
 
== References ==

Revision as of 21:12, 27 September 2006

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

Research topics

Results

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

Programmer, Server architect, and administrator; July 2005–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. [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.

External links

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