Weizhong
Li
The Burnham Institute, 10901
N. Torrey
Phone: (858) 646 3100 x 3553, Email liwz@burnham.org
o
Author of CD-
o
Author of an invited review paper of Trends in
biotechnology (2002)
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Invited speaker, 4th Annual
Integrated Bioinformatics conference (2002),
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Program committee for ISMB (2002),
Ph.D., Department
of Chemistry,
Advisor: Fangming Miao,
Thesis: Algorithm development of macromolecular electrostatics
and its applications on studies of structure, activity, stability and function
of modified enzymes
B.
S., Department of Chemistry,
The Burnham Institute,
Staff
scientist
o
Developing methods for automated large scale and
comprehensive protein annotation
Quorex Pharmaceuticals, Inc,
Bioinformatics
scientist, Staff scientist,
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Developed algorithm and annotation database for
anti-infective drug target discovery
o
Conducted Quorex IDEC
collaboration for large scale novel cancer drug target discovery
o
Developed methods for structural based drug
design projects and virtual screening
o
Managed company network, scientific software,
and databases
The Burnham Institute,
Postdoctoral
associate with Adam Godzik
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Developed software for large-scale automated
gene hunting, genome and sequence analysis
o
Developed tools and applied them in fold
recognition
o
Identified several novel genes
UCSD,
Postdoctoral
fellow with Adam Godzik
o
Developed algorithm for huge database sequence
clustering
o
Built bioinformatics web servers for protein
fold prediction
o
Conducted sequence analysis and 3D modeling of
some novel protein domains
Lecturer
for research and teaching
o
Set up and maintained the first
bioinformatics server in
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Maintained the PDB and
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Developed software and databases for protein
structure modeling and design
o
Advised graduate students in drug design and
protein modeling (1996-1999)
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Instructed “molecular modeling and drug design”
to graduate students (1998-1999)
o
Instructed structural chemistry to undergraduate
students (1997)
o
Manuscript reviewer for
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Editorial board of China Association of Science
and Technology 3rd Academic Conference of Young Scientist (1998)
o
Invited speaker, “Scent mountain” conference on
bioinformatics (1998) in
o
CD-
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Quorex dedicated
diverse virtual screening library (2 million unique compounds)
o
Q-eye, a package for multiple sequence and
structure comparison, visualization, and analysis
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Protein vision pathogenic bacteria genome
annotation databases
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Saturated BLAST, a effective tool for database
searching and novel gene discovery (http://bioinformatics.burnham.org/xblast)
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FFAS server and PDB-BLAST server, sensitive remote
homology detection and fold recognition tools, with automated comparative modeling function (http://bioinformatics.burnham-inst.org/pages/servers/index.html)
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Protein loop motif databases (http://mdl.ipc.pku.edu.cn/moldes/oldmem/liwz/home/loop.htm)
Selected Publications
1.
Discovering new genes with advanced homology detection.
Weizhong Li &
2.
Sequence clustering strategies improve remote homology
recognition while reducing search times. Weizhong
Li,
3.
Tolerating some redundancy significantly speeds up
clustering of large protein databases. Weizhong
Li,
4.
Clustering of highly homologous sequences to reduce the
size of large protein databases. Weizhong
Li,
5.
Saturated BLAST: An automated multiple intermediate
sequence search used to detect distant homology. Weizhong Li, Frederic Pio, Krzysztof Pawlowski &
6.
Exploring the conformational diversity of loops on conserved
frameworks. Weizhong Li, Shide Liang, Renxiao
Wang,
7.
Proteins loops on structurally similar scaffolds:
Database and conformational analysis. Weizhong Li, Zhijie
Liu &
Other Publications
8.
A residue in the S2 subsite
controls substrate selectivity of matrix metalloproteinase-2 and matrix
metalloproteinase-9. Emily Chen, Weizhong Li,
9.
Homotypic secretory
vesicle fusion induced by the protein tyrosine phosphatase
10.
A segment alignment approach to protein comparison. Yuzhen Ye,
11.
In the search for more accurate alignments in twilight
zone.
12.
Cysteine regulation
of protein function – as exemplified by NMDA receptor modulation. Stuart
Lipton, Yun-Beom Choi, Hiroto Takahashi, Dongxian Zhang,
Weizhong Li,
13.
Cloning and characterization of glucose transporter 11,
a novel sugar transporter that is alternatively spliced in various
tissues. Xiaohua Wu, Weizhong Li, Vandana Sharma,
14.
A unique substrate binding mode discriminates membrane
type 1-matrix metalloproteinase (MT1-MMP) from other matrix metalloproteinase.
Steven Kridel, Hisako Sawai,
Boris Ratnikov, Emily Chen, Weizhong Li ,
15.
A unique substrate recognition profile for matrix
metalloproteinase-2. Emily Chen, Steven J. Kridel,
Eric W. Howard, Weizhong Li ,
16.
Modeling the third loop of short-chain snake venom
neurotoxins: Roles of the short-range and long-range interactions. Zhijie Liu, Weizhong Li, Hongyu
Zhang, Yuzhen Han &
17.
Comparison of sequence profiles. Strategies for
structural predictions using sequence information. Leszek Rychlewski,
18.
Grafting of protein-protein interaction epiope. Shide Liang, Weizhong Li, Lan
Xiao, Jiansuo Wang &
19.
Calculation of protein surface loops using monte-carlo simulated annealing simulation. Zhijie Liu, Fenglou Mao, Weizhong Li, Yuzhen
Han &
20.
Construction of protein binding site in scaffold
structures. Shide Liang, Zhijie Liu, Weizhong
Li &
21.
Conformational changes accompanying with the binding of
protein and ligand. Zhijie
Liu, Lin Liang, Weizhong
Li, Yuzhen Han & Luhua
Lai. Acta. Chimica. Sinica (2000) 58:772-776
22.
Progress of Bioinformatics Database Services. Weizhong Li, Renxiao
Wang, Dawei Lin, Fenglou
Mao, Yuzheng Han & Luhua
Lai. Prog. Biochem. Biophys (1999) 26:22-26
23.
Rational screenning in
combinatorial peptide libraries of protein functional loop. Weizhong Li, Zhijie
Liu, Shide Liang, Yuzhen Han & Luhua Lai. Chinese Science Bulletin. (1999) 44:2150-2154
24.
Bioinformatics Server of
25.
A quantum and docking study of substituted deoxyuridines. Ming Sun, Weizhong Li, Ming Yu, Jinling Wang, Fangming Miao, I. Basnak, T.A. Hamor, & R.T.
Walker. Acta Physico-Chimica Sinica. (1999) 15:834-837
26.
Solvation Interaction and Stability
of Modified Superoxide Dismutase.
Weizhong Li & Fangming Miao. Acta Physico-Chimica Sinica. (1998) 14:289
27.
Estimating Binding Affinities for Enzyme-Ligand Complexes. Renxiao Wang, Weizhong Li, Luhua
Lai & Youqi Tang. Acta. Physico-Chimica Sinica.
(1998) 14:826
28.
Electrostatics and Stability of Modified Copper, Zinc Superoxide Dismutase. Weizhong Li & Fangming
Miao. Prog. Biochem. Biophys. (1996) 23:537
29.
Software Package of Electrostatics of MacroMolecules MMEP. Weizhong
Li, Jinling Wang, Xiaolan
Liu & Fangming Miao. HuaXue TongBao(Chinese)
(1996)
30.
Molecular Dynamic Simulation of Modified Copper, Zinc Superoxide Dismutase. Weizhong Li, Xiaolan
Liu, Jinling Wang & Fangming
Miao. Acta Scientiarum Natrualium Universitatis Nankaiensis.
(1996) 29:90
31.
1,4,10,13-Tetrathia-7,16-diazacyclooctadecanenickel(II)
Nitrate Hydrate. Wei-Zhong Li, Jin-Ling Wang, Xue-Sheng
Miao, You Zhou et al. Acta Cryst (1996) C52:555
32.
A study of complex of macrocyclic
polyethers containing S and N atoms: 1,4,10,13-tetrathia-7,16-diazacyclooctadecane with cupric
nitrate. Jin-Ling Wang, You Zhou, Xiu-Sheng Miao, Fang-Ming Miao & Wei-Zhong Li. Chinese J. Struc.
Chem. (1996) 15:171
33.
Dimethyl [a-(Benzylamino)-p-chlorobenzyl]phosphonate. Xiao-Lan Liu, You Zhou, Wei-Zhong Li, Zhi Fan et al. Acta Cryst. (1995) C51:2350