Projects and research interests
[Bioinformatics]
[Loop modelling]
[Loop design]
[Protein electrostatics]
[Other]
Bioinformatics
One of my major interest is Bioinformatics.
Now I maintain the
Peking University Bioinformatics Server in
our laboratory.
This server is the first
Bioinformatics Server in China.
The server has extensive information and resources on Biology and
related fields, especially for protein structure studies.
It is the official mirror site for
PDB
(The Brookhaven Protein Data Bank) and
SCOP
(Structural Classification of Proteins).
I also use many of these resources such as PDB, SCOP, DSSP, HSSP, FSSP,
CATH, Swiss-prot, BLAST, FASTA etc. for my research work
in protein structure prediction.
Protein Loop Modeling
Loop modelling is one of the key problems in protein structure studies.
Our aim here is to developing rational methods to predict loop structures.
I use both database searching and ab-initial calculating methods to model loops.
At present, I build a loop database
by searching the FSSP and PDB.
The database gives the structural diversity of loops on similar scaffolds.
The conformation features and sequence pattern are discussed in
the 84 motif families(version 1.0). Here is another
loop database
Another tool I used is
LPSA. LPSA is a program developed in our lab. using
Monto Carlo simulated annealing method to calculate conformation
of protein loops. It is a efficient algorithm.
Now I have improved this program, the new program is even faster and accurate.
Functional loop design
The further aim of loop modelling is to design functional loops to binding
a desired ligand. We first choose a native protein scaffold. On this scaffold,
we design a loop sequence, compute its comformation,
dock the ligand to this loop and its scaffold.
The procedure will screen the whole combinatorial loop libraries.
My co-workers and I have already finished most program modules including
loop conformation computing, sidechain growing, binding affinity prediction
and so on.
The next step is the to combine them to software package.
Protein Electrostatics
This is what I had done for my Ph. D.
The first part of this work was writting a program package named MMEP.
MMEP ,which based on the FDPB, can display various electrostatics
properties and calculate solvation energy, electrostatic interactions,
ionication states of charged residues of protein and so on.
MMEP was written in C and OpenGL.
Then I used this program to study stability and activity of modified enzyme.
I analyzed the correlation between stability and solvation energy and
other electrostatic energies. Also, the electrostatic interaction
between enzyme and substrate is calculated. The pH-dependent activity of
enzyme is computed.
Other
I also had miscellaneous molecular modelling experiences such as comparative
modelling, molecular dynamics simulation.