Biophysics and Computational Biology ????????? National Central University ?????????

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Biophysics and Computational Biology?????????
National Central University?????????

• ???
• Computational Biology Laboratory
• ???????
• CBL_at_NCU
• 2002 January 24

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The Human Genome Project??????

• 1988 ??(?????????)??
• ??
• ???????????????
• ????????
• ??????????????
• ??2005??????????

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• Millions of base pairs of DNA

Millions of sequences
(As of 2002 January 13)
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1995-2005 About 100 bacterial genomes ??
0.5-9 Mb hundreds to 2000
genes 1996 April Yeast (Saccharomyces
cerevisiae) 12 Mb, 5,500
genes ?? 1998 Dec. -Worm
(Caenorhabditis elegans)
97 Mb, 19,000 genes ?? 2000 March
- Fly (Drosophila melanogaster)
137 Mb, 13,500 genes ?? 2000
Dec. - Mustard (Arabidopsis thaliana)
125 Mb, 25,498 genes
?? 2000 June Human (Homo sapiens) 1st rough
draft 2001 Feb 15/16 Human, working draft
?? 3000 Mb, 35,00040,000
genes ??????????????
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???????2001?2???????
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??? (Genome) ??????????
DNA - ?????? ?????? ????? - A,C,G,T ???? -
???? ????? ??? ?????? DNA
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?????????????

• in vivo ????
• in vitro ????
• in silico ????

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Life Science in silico ?????????
CBL_at_NCU
biology ?? computer-science
?? math physics
??
It is much easier to teach biology to people
from a math, physics or computer-science
background than to teach a biologist how to
code well. - Nature,
February 15, 2001, p963
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Bioinformatics ????Biophysics ????
Computational Biology ????

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• DNA??? ?????
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• ???????DNA????????
• DNA???????
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• DNA???????
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Molecular evolution and Genome evolution

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http//www.ncbi.nlm.nih.gov/PMGifs/Genomes/micr.ht
ml
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1 tgctgagaaa acatcaagctg tgtttctcct
tccccaaag acacttcgca gcccctcttg 61
ggatccagcg cagcgcaagg taagccagat gcctctgctg
ttgccctccc tgtgggcctg 121 ctctcctcac
gccggccccc acctgggcca cctgtggcac ctgccaggag
gctgagctgc 181 aaaccccaat gaggggcagg
tgctcccgga gacctgcttc ccacacgccc atcgttctgc
241 ccccggcttt gagttctccc aggcccctct gtgcacccct
ccctagcagg aacatgccgt 301 ctgccccctt
gagctttgca aggtctcggt gataatagga aggtctttgc
cttgcaggga 361 gaatgagtca tccgtgctcc
ctccgagggg gattctggag tccacagtaa ttgcagggct
421 gacactctgc cctgcaccgg gcgccccagc tcctccccac
ctccctcctc catccctgtc 481 tccggctatt
aagacggggc gctcaggggc ctgtaactgg ggaaggtata
cccgccctgc 541 agaggtggac cctgtctgtt
ttgatttctg ttccatgtcc aaggcaggac atgaccctgt
601 tttggaatgc tgatttatgg attttccagg ccactgtgcc
ccagatacaa ttttctctga 661 cattaagaat
acgtagagaa ctaaatgcat tttcttctta aaaaaaaaaa
aaaccaaaaa 721 aaaaaaaaaa aaaccaaaaa
actgtactta ataagatcca tgcctataag acaaaggaac
781 acctcttgtc atatatgtgg gacctcgggc agcgtgtgaa
agtttacttg cagtttgcag 841 taaaatgaca
aagctaacac ctggcgtgga caatcttacc tagctatgct
ctccaaaatg 901 tattttttct aatctgggca
acaatggtgc catctcggtt cactgcaacc tccgcttccc
961 aggttcaagc gattctccgg cctcagcctc ccaagtagct
gggaggacag gcacccgcca 1021 tgatgcccgg
ttaatttttg tatttttagc agagatgggt tttcgccatg
ttggccaggc 1081 tggtctcgaa ctcctgacct
caggtgatcc gcctgccttg gcctcccaaa gtgctgggat
1141 gacaggcgtg agccaccgcg cccagccagg aatctatgca
tttgcctttg aatattagcc 1201 tccactgccc
catcagcaaa aggcaaaaca ggttaccagc ctcccgccac
ccctgaagaa 1261 taattgtgaa aaaatgtgga
attagcaaca tgttggcagg atttttgctg aggttataag
1321 ccacttcctt catctgggtc tgagcttttt tgtattcggt
cttaccattc gttggttctg 1381 tagttcatgt
ttcaaaaatg cagcctcaga gactgcaagc cgctgagtca
aatacaaata 1441 gatttttaaa gtgtatttat
tttaaacaaa aaataaaatc acacataaga taaaacaaaa
1501 cgaaactgac tttatacagt aaaataaacg atgcctgggc
acagtggctc acgcctgtca
??? ????
A stretch of genome from the X chromo- some of
Homo sapien http// www.ncbi.nlm.nih.gov/ entrez
/viewer.fcgi?val 2276452db Nucleotide dopt Ge
nBank The complete genome has 2,000,000
such Pages
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10??? 20??? 30??? 40???
WF Doolittle, Proc. Natl. Acad. Sci. USA, Vol.
94, pp. 1275112753 (1997)
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?????/ DNA???????/???????
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Black genome data green random sequence red
model sequence data
Red symbols Universal genome growth model based
on maximally stochastic segmental duplication.
Has many implications in early history of
genomes and evolution.
Lroot L/Ms is a universal constant Universality
class (red line) log Lroot ak B a 0.398,
B 1.61 (30)
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???????????? Molecular dynamics simulation of
Protein Structure Function
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• ?10?flop/??PC???????

HIV???? (562????)
CBL_at_NCU
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?????????????????Massively Distributed
Computingand An NRPGM ProjectonProtein
Structure and Function
Computation Biology LabPhysics Dept Life
Science DeptNational Central University
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Multi-temperature Annealing (II)
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MD simulation of n3 peptide
RMSD (nm)
time (ps)

• helix in stand-alone n3 supposed to unwind and
  then refold to hairpin
• More running time needed to ascertain results of
  Kozin et al.

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???? Magnetic and Electric Brain waves
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• The problem better method for analyzing
  magnetoencephalogram (MEG) data
• The method maximum entropy method

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Computation Biology Laboratory (2004)
??!????????Google HC Lee
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There are 24 humanchromosomes
Human has 23 chromosomes
There are 24 human chromosomes ??? ????
???
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• ????????????DNA??????
• ?????????,???????,??????DNA?????
• ???????DNA
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Haemophilus influenzae ????
CBL_at_NCU University of British Columbia