Difference between revisions of "Dr. Carlos J. Camacho Laboratory"
From Christoph's Personal Wiki
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* [http://en.wikipedia.org/wiki/Molecular_docking Molecular docking] | * [http://en.wikipedia.org/wiki/Molecular_docking Molecular docking] | ||
* [http://en.wikipedia.org/wiki/Protein-ligand_docking Protein-ligand docking] | * [http://en.wikipedia.org/wiki/Protein-ligand_docking Protein-ligand docking] | ||
| − | * [http://en.wikipedia.org/wiki/Rigid_body_dynamics Rigid body dynamics] | + | * [http://en.wikipedia.org/wiki/Rigid_body_dynamics Rigid body dynamics] (see also: [http://www.d6.com/users/checker/dynamics.htm]) |
* [http://en.wikipedia.org/wiki/Molecular_mechanics Molecular mechanics] | * [http://en.wikipedia.org/wiki/Molecular_mechanics Molecular mechanics] | ||
* [http://en.wikipedia.org/wiki/Search_algorithm Search algorithm] | * [http://en.wikipedia.org/wiki/Search_algorithm Search algorithm] | ||
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** [http://en.wikipedia.org/wiki/Trace_%28linear_algebra%29 Trace (linear algebra)] | ** [http://en.wikipedia.org/wiki/Trace_%28linear_algebra%29 Trace (linear algebra)] | ||
** [http://en.wikipedia.org/wiki/Moment_of_inertia Moment of inertia] (inertia tensor matrix) | ** [http://en.wikipedia.org/wiki/Moment_of_inertia Moment of inertia] (inertia tensor matrix) | ||
| + | ** [http://www.orbitals.com/self/least/least.htm General Least-Squares] | ||
== Results == | == Results == | ||
Revision as of 02:24, 25 August 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
- 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
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.
