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

Revision as of 02:12, 20 June 2007

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

• Protein-protein docking (Rigid body)
• Protein-protein interaction prediction
• Protein structural alignment
• Molecular docking
• Protein-ligand docking
• Rigid body dynamics (see also: [1])
• Molecular mechanics
• Search algorithm
• Katchalski-Katzir algorithm
• DOT — a molecular interaction programme
• Fast Fourier transform — used in the DOT algorithm
• Convolution theorem
• Van der Waals radius
• Force fields
• MPI / MPICH — for parallel computing
• Mathematics:
  • Determinant (linear algebra)
  • Minor (linear algebra) (cofactor)
  • Trace (linear algebra)
  • Moment of inertia (inertia tensor matrix)
  • General Least-Squares
  • Rotation matrix
  • Euler angles
  • Euler's equations

Results

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

• FastContact Server: a free energy scoring tool for protein-protein complex structures.

Version 1.0: Programmer, Server architect, and administrator; July 2005–December 2006.

Version 2.0: Programmer, Server architect, and administrator; January 2007-present.

• SmoothDock Server (currently under development):

Programmer, Server architect, and administrator; January 2005–present (note: This server uses code optimised and run in parallel on 256 processors).

• LooseLoops Server (currently under development and construction):

Programmer, Server architect, and administrator; November 2004–present.

• DomainSplit Server:

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.

External links

• Dr. Carlos J. Camacho Laboratory website