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 and from March 2006 - present (in absentia).
Research topics
- Protein-protein docking (Rigid body)
- Protein-protein interaction prediction
- Protein structural alignment
- Molecular docking
- Protein-ligand docking
- 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
Results
The research I have done in the laboratory has, so far, yielded a paper published and four Web Servers:
- FastContact Server: a free energy scoring tool for protein-protein complex structures.
- Programmer, Server architect, and administrator; July 2005–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.
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. [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.
- Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z (2005). Protein-Protein Docking Benchmark 2.0: an Update. Proteins.
- Proteins: Structure, Function, and Genetics (special edition) Volume 52, Issue 1, 2003, all pages.
