My research area is the bioinformatic analysis of protein 3D structures :
- 3D structure prediction
- local structure and secondary structure prediction
- secondary structure assignment
- local protein topology
- contacts within structures
- protein-protein interactions
PhD Thesis, INRA Jouy-en-Josas
I defended my thesis, entitled "Protein local structure prediction
using hidden Markov models" in november 2005.
During my thesis, I developped methods based on hidden Markov models (HMM) to
predict protein secondary structure and also the classical dihedral angles
formed by the protein backbone (Martin et al, BMC Struct Biol, 2006).
This work implied to derive a methodology to build and
select approriate HMM
(Martin et al, IEEE Intelligent System, 2005 and Martin et al, BMC struct Biol, 2006).
When working on secondary structures, I became interested
in the question of secondary structure assignment.
I developped an assignment method, called KAKSI, which is very efficient
to detect local distorsion within helices and strands (kinks).
(Martin et al, BMC Struct Biol, 2005).
Visit my thesis webpage "Protein local structure prediction using hidden Markov models".
Research at EBGM, Paris 7 University
During my post-doctoral period at EBGM, I mainly worked on two projects:
- Structural study of Outer Membrane Proteins using a specific HMM-based structural alphabet
- Characterization of contacts within protein 3D structures with the structural alphabet developped by Camproux et col.
Research Indian Institute of Science, Bangalore
During my post-doctoral period at IISc in Pr Srinivasan team, I mainly worked on two projects:
- Comparison of human and chimpanzee protein kinases.
- Classification of protein kinases.