Difference between revisions of "Dr. Carlos J. Camacho Laboratory"
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The '''Dr. Carlos J. Camacho Laboratory''' is where I did [[:Category:Academic Research|scientific research]] from October 2004 - July 2005, from March 2006 - September 2006 (''in absentia''), and from December 2006 - February 2007 (''in absentia''). | The '''Dr. Carlos J. Camacho Laboratory''' is where I did [[:Category:Academic Research|scientific research]] from October 2004 - July 2005, from March 2006 - September 2006 (''in absentia''), and from December 2006 - February 2007 (''in absentia''). | ||
| − | == Research topics == | + | ==Research topics== |
* [http://en.wikipedia.org/wiki/Protein-protein_docking Protein-protein docking] (Rigid body) | * [http://en.wikipedia.org/wiki/Protein-protein_docking Protein-protein docking] (Rigid body) | ||
* [http://en.wikipedia.org/wiki/Protein-protein_interaction_prediction Protein-protein interaction prediction] | * [http://en.wikipedia.org/wiki/Protein-protein_interaction_prediction Protein-protein interaction prediction] | ||
| Line 18: | Line 18: | ||
* [http://en.wikipedia.org/wiki/Message_Passing_Interface MPI] / [http://en.wikipedia.org/wiki/MPICH MPICH] — for parallel computing | * [http://en.wikipedia.org/wiki/Message_Passing_Interface MPI] / [http://en.wikipedia.org/wiki/MPICH MPICH] — for parallel computing | ||
* Mathematics: | * Mathematics: | ||
| − | ** [http://en.wikipedia.org/wiki/Determinants Determinant (linear algebra)] | + | **[http://en.wikipedia.org/wiki/Determinants Determinant (linear algebra)] |
| − | ** [http://en.wikipedia.org/wiki/Minor_%28linear_algebra%29 Minor (linear algebra)] (cofactor) | + | **[http://en.wikipedia.org/wiki/Minor_%28linear_algebra%29 Minor (linear algebra)] (cofactor) |
| − | ** [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] | + | **[http://www.orbitals.com/self/least/least.htm General Least-Squares] |
| + | **[[wikipedia:Rotation matrix|Rotation matrix]] | ||
| + | **[[wikipedia:Euler angles|Euler angles]] | ||
| + | **[[wikipedia:Euler's equations|Euler's equations]] | ||
== Results == | == Results == | ||
Revision as of 02:09, 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).
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 a paper published[1] 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. [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.
