Difference between revisions of "Dr. Carlos J. Camacho Laboratory"
From Christoph's Personal Wiki
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== Results == | == Results == | ||
| − | The research I have done in the laboratory has, so far, yielded a [[Curriculum_Vitae#Publications|paper published]] and four Web Servers: | + | The research I have done in the laboratory has, so far, yielded a [[Curriculum_Vitae#Publications|paper published]]<ref name=Camacho2006>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. [http://www3.interscience.wiley.com/cgi-bin/abstract/112467717/ABSTRACT?CRETRY=1&SRETRY=0 ''Proteins, 63(4):868-77'']. [[http://www.hubmed.org/display.cgi?uids=16506242 HubMed]]</ref> and four Web Servers: |
* '''[[FastContact|FastContact Server]]''': a free energy scoring tool for protein-protein complex structures. | * '''[[FastContact|FastContact Server]]''': a free energy scoring tool for protein-protein complex structures. | ||
:: Programmer, Server architect, and administrator; July 2005–present. | :: Programmer, Server architect, and administrator; July 2005–present. | ||
| Line 36: | Line 36: | ||
== Benchmarks == | == Benchmarks == | ||
| − | A benchmark of 84 protein-protein interactions with known complexed structures has been developed for testing docking methods<ref>Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z (2005). Protein-Protein Docking Benchmark 2.0: an Update. ''Proteins, 60(2):214-6''.</ref>. The set is chosen to cover a wide range of interaction types, and to avoid repeated features, such as the profile of interactors' structural families according to the [http://scop.mrc-lmb.cam.ac.uk/scop/ SCOP] database. Benchmark elements are classified into three levels of difficulty (the most difficult containing the largest change in backbone conformation). The protein-protein docking benchmark contains examples of enzyme-inhibitor, antigen-antibody and homomultimeric complexes. | + | A benchmark of 84 protein-protein interactions with known complexed structures has been developed for testing docking methods<ref name=Minteris>Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z (2005). Protein-Protein Docking Benchmark 2.0: an Update. ''Proteins, 60(2):214-6''.</ref>. The set is chosen to cover a wide range of interaction types, and to avoid repeated features, such as the profile of interactors' structural families according to the [http://scop.mrc-lmb.cam.ac.uk/scop/ SCOP] database. Benchmark elements are classified into three levels of difficulty (the most difficult containing the largest change in backbone conformation). The protein-protein docking benchmark contains examples of enzyme-inhibitor, antigen-antibody and homomultimeric complexes. |
== References == | == References == | ||
| − | + | <references/> | |
=== Further reading === | === 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''. | * 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''. | * 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. | * Proteins: Structure, Function, and Genetics (special edition) Volume 52, Issue 1, 2003, all pages. | ||
Revision as of 19:16, 16 September 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[1] 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.
Benchmarks
A benchmark of 84 protein-protein interactions with known complexed structures has been developed for testing docking methods[2]. The set is chosen to cover a wide range of interaction types, and to avoid repeated features, such as the profile of interactors' structural families according to the SCOP database. Benchmark elements are classified into three levels of difficulty (the most difficult containing the largest change in backbone conformation). The protein-protein docking benchmark contains examples of enzyme-inhibitor, antigen-antibody and homomultimeric complexes.
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]
- ↑ Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z (2005). Protein-Protein Docking Benchmark 2.0: an Update. Proteins, 60(2):214-6.
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.
