Dr. Carlos J. Camacho Laboratory
From Christoph's Personal Wiki
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).
Contents
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.
- 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
- ↑ 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]
- ↑ 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.
