homology modeling lu chih-hao 1. why study protein structure? proteins play crucial functional roles...
TRANSCRIPT
![Page 1: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/1.jpg)
Homology Modeling
Lu Chih-Hao
1
![Page 2: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/2.jpg)
Why study protein structure?
• Proteins play crucial functional roles in all biological processes: enzymatic catalysis, signaling messengers …
• Function depends on 3D structure.
• Easy to obtain protein sequences, difficult to determine structure.
2
![Page 3: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/3.jpg)
Where find the data?
• Protein Data Bank (PDB)– http://www.rcsb.org/pdb/– > ~65,500 structures of proteins
• Text file contain: coordinates for each heavy atom from the first residue to the last
X Y Z
3
![Page 4: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/4.jpg)
PDB Statistics
4
![Page 5: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/5.jpg)
TIM barrel
5
![Page 6: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/6.jpg)
How to determine the protein structure?
• By experimentation– X-Ray– NMR (nuclear magnetic resonance spectroscopy)
• Sequence-Structure gap
6
![Page 7: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/7.jpg)
Protein Structure Prediction
• The primary sequence already contain all the information necessary to define 3D structure.
• The 3D protein structure can be predicted according to three main categories of methods (Rost & O’Donoghue, 1997): (1) homology modeling; (2) fold recognition (threading); (3) ab initio techniques.
• Homology modeling is currently the most accurate method to predict protein 3D structure (Tramontano, 1998).
7
![Page 8: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/8.jpg)
Protein Structure Prediction
Sequence
Sequence HomologyTo known fold
HomologyModeling
>30%
Threading
Match Found?
Ab initio
No
Model
Yes
<30%
8
![Page 9: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/9.jpg)
.
0
20
40
60
80
100
0 50 100 150 200 250
identity
Number of residues aligned
Perc
enta
ge s
equence
identi
ty/s
imila
rity
(B.Rost, Columbia, NewYork)
Sequence identity implies structural similarity
Sequence similarity implies structural similarity?
Safe zone
9
![Page 10: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/10.jpg)
Homology Modeling
• Basis– Structure is much more conserved than sequence
during evolution
• Limited applicability– A large number of proteins and ORFs have no
similarity to proteins with known structure
10
![Page 11: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/11.jpg)
??
KQFTKCELSQNLYDIDGYGRIALPELICTMFHTSGYDTQAIVENDESTEYGLFQISNALWCKSSQSPQSRNICDITCDKFLDDDITDDIMCAKKILDIKGIDYWIAHKALCTEKLEQWLCEKE
Use as template
8lyz1alc
KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRLShare Similar
Sequence
Homologous
What is Homology Modeling?
Target Template
11
![Page 12: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/12.jpg)
Structure prediction by homology modeling
12
Step 1
Step 2
Step 3
Step 4
![Page 13: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/13.jpg)
Homology detection and template selection
• Homology detection– To detect the fold of a probe sequence from a library
of known target fold.
• The three type of sequence based methods:– Pair-wise sequence-sequence comparison
• FASTA, BLAST
– Sequence profile comparison• PSI-BLAST, IMPALA, HMMER, SAM
– Profile-profile comparison• prof_sim, COMPASS
13
![Page 14: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/14.jpg)
Q T
Sequence-Sequence comparison
BLAST, FASTA, SSEARCH
14
![Page 15: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/15.jpg)
Q T
Profile-Sequence comparison
PSI-BLAST15
![Page 16: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/16.jpg)
PSI-BLAST Overview
16
![Page 17: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/17.jpg)
Q T
Sequence-Profile comparison
RPS-BLAST, IMPALA, HMMER, SAM
17
![Page 18: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/18.jpg)
Q T
Profile-Profile comparison
prof_sim, COMPASS18
![Page 19: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/19.jpg)
Method_11lmb3 <-> 1pou shift = 9.34 σ = 39.62LEDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKVSVEEFSPSIAREIYEMYEAHHHHHHHHHHHHHHHHHCCCChhhhhhhhccchhhhhhhhccccccchhhhhhhhhhhccchhhcchhhhhhhhhhhhh||||||||||||||||||||| ++++++++ + ++++++++++++ ++++++++000000000000000000000 99999999 X XXXXXXXXXXXX XXXXXXXXHHHHHHHHHHHHHHHHHHCCC---------cchhhhhhhhhcccccc---chhhhhhhcccccccchhhhhhhhhhhhhLEELEQFAKTFKQRRIKLGFT---------QGDVGLAMGKLYGNDFS---QTTISRFEALNLSFKNMCKLKPLLEKWLN
Method_21lmb3 <-> 1pou Shift = 0.67 σ = 60.78LEDARRLKAIYEKKKNELGLS----QESVADKMG--MGQSGVGALFN-GINALNAYNAALLAKILKVSVEEFSHHHHHHHHHHHHHHHHHCCCC----hhhhhhhhc--cCHHHHHHHHC-cccccchhhhhhhhhhhccchhhcc||||||||||||||||||||| ---- |||||||||| -- ++++++++ ++ 000000000000000000000 4444 0000000000 11 11111111 44 HHHHHHHHHHHHHHHHHHCCCcchhhhhhhhhcccccCCHHHHHHHCccccccchhhhhhhhhhh---hhhccLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLEKW---LNDAE
The importance of the sequence alignment
SCR; structure conserved region SVR; structure variable region
19
![Page 20: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/20.jpg)
Backbone generation
• Rigid-body assembly– Building model core
20
![Page 21: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/21.jpg)
21
![Page 22: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/22.jpg)
Construction of loops might be done by:
Wedemeyer,ScheragaJ. Comput. Chem.20, 819-844(1999)
Ab initio methods - without any prior knowledge. This is done by empirical scoring functions that check large number of conformations and evaluates each of them.
22
![Page 23: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/23.jpg)
data clustereddata
library
Construction of loops might be done by:
Using database of loops which appear in known structures. The loops could be categorized by their length or sequence
23
![Page 24: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/24.jpg)
Scan database and search protein fragments with correct number of residuesand correct end-to-end distances
24
![Page 25: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/25.jpg)
25
![Page 26: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/26.jpg)
26
![Page 27: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/27.jpg)
Loop length
cRM
S (Ǻ
)
Method breaksdown for loopslarger than 9
Loop Modeling: A database approach
27
![Page 28: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/28.jpg)
GDT_TS = 45.96 GDT_TS = 60.48
Predicted model with long loop Without loop
Target: 2bj7A
28
![Page 29: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/29.jpg)
29
![Page 30: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/30.jpg)
Errors in Homology Modeling
a) Side chain packing b)Distortions and shifts c) No template
Template ModelTrue structure30
![Page 31: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/31.jpg)
Errors in Homology Modeling
d) Misalignments e) Incorrect template
(Marti-Renom et al., 2000)
Template ModelTrue structure31
![Page 32: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/32.jpg)
PROCHECK, Verify3D, Prosa, Anolea, Bala …
32
![Page 33: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/33.jpg)
PROCHECK
β
α http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html
33
![Page 34: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/34.jpg)
Verify3D
• Verify3D analyzes the compatibility of an atomic model (3D) with its own amino acid sequence (1D).
Luethy et al., 1992 34
![Page 35: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/35.jpg)
ProQ Server
• ProQ is a neural network-based predictor
– Structural features quality of a protein model.
Arne Elofssons group: http://www.sbc.su.se/~bjorn/ProQ/
Correct Good Very goodLGscore > 1.5 LGscore > 3 LGscore > 5MaxSub > 0.1 MaxSub > 0.5 MaxSub > 0.8
35
![Page 36: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/36.jpg)
Modeling accuracy
(Marti-Renom et al., 2000)
36
![Page 37: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/37.jpg)
Utility of Structural Information
37
![Page 38: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/38.jpg)
38
![Page 39: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/39.jpg)
39
![Page 40: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/40.jpg)
(PS)2: protein structure prediction server
40
![Page 41: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/41.jpg)
Consensus strategy
• The idea of consensus analysis is to gather predictions from a set of different methods.
• The performance of consensus methods is significantly higher than for individual methods.
3d-shotgun (Fischer D., 2003)3d-jury (Ginalski K et al., 2003)Pmodeller (Bjorn W et al., 2003)
41
![Page 42: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/42.jpg)
Structure prediction by homology modeling
42
Step 1
Step 2
Step 3
Step 4
![Page 43: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/43.jpg)
Figure 1. Overview of the protein structure prediction server, (PS)2.
Overview of the (PS)2 method
Step1: Template search/selection by the
consensus of PSI-BLAST and IMPALA
Step2: Target-template alignment by the consensus of T-Coffee, PSI-BLAST,
and IMPALA
Step3: Model building by MODELLER and structure evaluation and visualization
by CHIME and Raster3D
(d)
(a)
(b) (c)
43
![Page 44: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/44.jpg)
: Aligned path of PSI-BLAST
: Aligned path of T-Coffee
: Aligned path of IMPALA
: Final aligned path
9: aligned in 1st cycle7: aligned in 2nd cycle5: aligned in 3rd cycle3: aligned in 4th cycle4 and 2: unfeasible solution
Input: target and template sequences
Output: target-template aligned sequences
Step 1: Initial all entries of the aligned matrix to 0. Align target and template sequences using PSI-BLAST, IMPALA, and T-Coffee.
Step 2: Sum aligned scores of these three alignments for each position with different scoring weights.
Step 3: Take the positions with the highest score as the aligned points to build the final target-template alignment. (e.g., the highest scoring is 9 for the 1st cycle in (b) )
Step 4: Identify the unfeasible positions. ( 4 and 2 in (b))
Step 5: Change the scores of unfeasible positions and the aligned points to 0.
Step 6: Repeatedly Steps 3 and 5 until all entries are 0.
Step 7: Output the path with the aligned points as the target-template alignment
(b)(a)
Alignment method
44
![Page 45: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/45.jpg)
http://predictioncenter.org/
45
![Page 46: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/46.jpg)
CASP3 servers registered:
1. 3D-PSSM (Sternberg) [email protected] 2. Karplus [email protected] 3. frsvr (Fischer) [email protected] 4. pscan (Eloffson) [email protected] 5. BASIC (Godzik) [email protected] 6. GenTHREADER [email protected] 7. Valentina di Francesco [email protected] 8. TOPITS (Rost) [email protected] 9. Bork
46
![Page 47: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/47.jpg)
CASP8 servers registered:
47
![Page 48: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/48.jpg)
}8 4, 2, 1,{(%)4
100_
dN
GDT
TSGDT d
d
- N is the total number residues of the target (native structure)- GDTd is the number of aligned residues whose Cα-atom distance
between the target and predicted model is less than d- d is 1, 2, 4, or 8 Å.
Model Evaluation
• Performance evaluation– Comparing the 47 CM targets to evaluate the
performance with the other groups in CASP6.
• GDT_TS Score
48
![Page 49: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/49.jpg)
10 272
6 294 Native structure
PSI-BLAST modelGDT_TS = 64.97
272(PS)2 modelGDT_TS = 67.22
GDT_TS = 66.00
10
10 272 IMPALA modelGDT_TS = 63.32
294 T-Coffee modelGDT_TS = 65.14
T0264 (1wde)
Aligned rate: 91.00 %
Aligned rate: 91.00 %
Aligned rate: 100 %6
Aligned rate: 100 %6 294
Figure 3. Comparison (PS)2 with PSI-BLAST, IMPALA, and T-Coffee of the prediction accuracies (global / local GDT_TS scores) on target T0264.
49
![Page 50: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/50.jpg)
Figure 4. Comparison of (PS)2 models with all automated servers in CASP6.
0
20
40
60
80
100
T0196
T0199_1
T0200
T0204
T0205
T0208
T0211
T0222_1
T0223_1
T0226
T0226_1
T0229
T0229_1
T0229_2
T0231
T0233
T0233_1
T0233_2
T0234
T0235_1
T0240
T0246
T0247
T0247_1
T0247_2
T0247_3
T0264
T0264_1
T0264_2
T0266
T0267
T0268
T0268_1
T0268_2
T0269
T0269_1
T0269_2
T0271
T0274
T0275
T0276
T0277
T0279
T0279_1
T0279_2
T0280_1
T0282
Targets
GD
T_T
S Sc
ore
(%)
50
![Page 51: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/51.jpg)
51
Table 1. Compare with the other groups in CASP6
(PS)2 RBTA ESYP 3DJR MGTH 3DJS PROS PMO5 PRCM PCO5 PCOB
Average GDT_TS
65.89 64.92 63.14 62.54 61.27 61.08 58.11 57.93 57.62 56.37 37.57
• Cases
T0269, Template 1prxA(PS)2 model, GDT_TS: 85.76
T0269, Template 1qq2AESYP model, GDT_TS: 78.48
![Page 52: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/52.jpg)
http://ps2.life.nctu.edu.tw
52
![Page 53: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/53.jpg)
53
![Page 54: Homology Modeling Lu Chih-Hao 1. Why study protein structure? Proteins play crucial functional roles in all biological processes: enzymatic catalysis,](https://reader035.vdocument.in/reader035/viewer/2022062802/56649ed05503460f94bdef62/html5/thumbnails/54.jpg)
54