NASA Technical Reports Server (NTRS) 20030017995: Website on Protein Interaction and Protein Structure Related Work

52 Pages·2 MB·English

by  NASA Technical Reports Server (NTRS)

Computational Bio-nanotechnology
i/ dB
Home Research Publications
RESEARCH:
In today's world, three seemingly diverse fields - computer information
technology, nanotechnology and biotechnology are joining forces to
enlarge our scientific knowledge and solve complex technological
problems. Our group is dedicated to conduct theoretical research
exploring the challenges in this area.
GROUP MEMBERS:
Manoj Samanta
Shoudan Liang
Home We collaborate with researchers from Stanford, Caltech, Uconn Health
Research Center, UCSF Medical School, Pennsylvania State University
University of Virginia School of Medicine, and University of
Publications Washington.
MAJOR AREAS:
Yeast Protein Interactions
Protein Structures
Current Transport through Small Molecules
We are part of the nanotechnology teem at NASA Ames Research
Center.
Nanotechnology at Astrobiology at NASA
NASA main page Ames Research Center
NASA Ames Ames
Please email [email protected] with any comment or suggestion on this website.
Analysis of Protein Interaction Data from Yeast
NAB
Horne Research Publications
RESEARCH:
Currently we are trying to understand the yeast proteome. There are
several experimental studies exploring the technology, nanotechnology
and biotechnology are joining togethe: to solve scientific and
technological problems. Our group is dedicated to theoretical research
exploring this challenging new direction of science.
MAJOR AREAS:
Common Partners of Protein
In this work, we analyze the common partners of protein to find any
statistical significance.
Home
Research Global Analysis of Protein Interaction Network
Publications In this work, we analyze the protein interaction network using a
percolation based method for long range order.
Nanotechnology at Astrobiology at NASA
NASA main page Ames Research Center
NASA Ames Ames
Please email [email protected] with any comment or suggestion on this website.
Common Partners of Proteins
N, JB
Home Research Publications
RESEARCH:
In this work, we start with two-protein interaction data of yeast
available from the DIP database and conduct an analysis based on the
number of common partners every psirs of proteins share. The
interactions are ranked based on their probabilities of occurance in a
random sample and then significant pairs are studied for interesting
patterns. More details about the method and observations are provided
in this publication.
You can download the top 8000 pairs from our dataset from here -plain
text, html.
Or enter any protein-name or ORF in the form below to get a list of
Home
other proteins it prefers to share partners with.
Research
Publications
To download our paper on this, click here.
Nanotechnology at Astrobiology at NASA
NASA main page Ames Research Center
NASA Ames Ames
Please email [email protected] with any comment or suggestion on this website.
Top 8000 Pairs
Home Research Publications
I
t 1-250 t 251-500 501-750 i 751-1000
I1001-1250 11251-1500 1501-1750 i1751-2000
i2001-2250 [2251-2500 2501-2750 I2751.3000
I 3001-3250-- t 3251-3500 3501-3750 "i3751-4000
t
I4001-4250 I4251-4500 4501-4750 14751-5000
Hom_
5501-5750 I5751-6000
Research
6751-7000"
Publications
7501-7750 I 7751-8000
NASA main page An-_es Research Center Nanotechnology at Astrobi¢,logy at NASA
NASA Ames Ames
Please email [email protected] with any comment or suggestion on this website.
Protein Pairs and Probabilities of Partners
Protein 1 # Partners Protein 2 # Partners Common Prob.
19 19 -47.406640
MYO3 [-] [C] MYO5 [-] [C] 4_/__ 25
25 21 -46.116416
ROX3 [-] [B] _ SRB6 [+] [T] _! 30
34 26 -45.496602
KRR1 [+] [U] _ PWP2 [+J [C] __ 57
25 20 -44.938714
ROX3 [-] [B] _ MED2 [-] [T] _ 26
26 20 -42.189077
MED2 [-] IT] SRB6 [+] [T] '_ 30
17 -42.174090
ATP1 [-] [E] _- '_ 18 ATP2 [-] [E] _! 22
39 -41.254598
KAP95 [+] [O] _ 57 1 SRP1 [+] [O] _!' 196
22 -40.575226
PRE1 [+] [F] _ 35 l RPN10 [-] [F] _! 37
30 22 -40.332938
YNL110C [+] [U] YKR081C [+] [U] _ 45
30 20 -40.077194
RPT1 [+] IF] RPN6 [+] [F] _ 30
33 21 -39.470885
SMX2 [-] IT] _ SMX3 [+] IT] _ 35
RPT1 [+] [F] 3O RPN5 [+] [F] _ 42 21 -38.501792
45 24 -38.256150
YKR081C [+] [U] _ NOP2 [+] IT] _ 48
30 22 -38.061850
RPN6 [+] [F] _ RPT3 [+] [F] _ 54
37 22 -38.043439
RPN10 [-] [F] RPN5 [+] IF] _ 42
30 2O -37.359955
RPN6 [+] [F] RPN10 [-] IF] _ 37
19 -36.579457
NUP49 [+] [O] _ 25 NUP57 [+] [O] _ 39
17 -36.507398
CKA2 [-] [T] _ 22 CKB1 [-] [T] _ 27
30 19 -36.389975
SRB6 [+] [T] MED7 [+] [B] _ 32
2O 16 -36,337854
YFR024C [-] [U] _ I YSC84 [-] [U] _ 23
30 20 -35.855384
RPN6 [+] [F] RPN5 [+] [F] _ 42
30 nn_ ,._ ,_ _ 54 21 -35.526602
- L J L J
RPT1[+]IF] 3O
' RPT3 [+] [F] i 54 2t -35.526602
!
30
RPTI [+] [F] _
RPN10 [-] [F] 37 19 -34.688605
34
KRR1 [+] [U] _
_LYGR090W [+] [U] _ 51 21 -34.380951 _
45
YKR081C [+] [U]
iYMR049C [+] [U] _i
PRE1[+][F] 35 i 42 1824
RPN5 [+] [F] J-33.83
SSF1 [-] [C] _ 26 t _ 48 19 -33.793427
t NOP2 [+] [TJ l"'
r_ 14
UBP6 [-] [F] iI RPN12 [+] [F] _ 26 14 -33.46529!
q
48
NOP2 [+] IT]
YMR049C [+] [U] '_ 55 23 -33.318364
26
RPN 12 [+] IF] _ I _ 30 17 -33.287209
RPN6 [+] IF]
YDa060W[+][P] _ t 28
NOP4 [+] IT] _lli_ 38 18 -32.638473
uEo2Hm 26
MED7 [+] [B] _ 32 17 -32.614595
RPN10 [-] [F] _" 37
RPT3 [+] _I 54 21 --32"593992
IF]
YKL059C [+] [U] _ 16
CFT2 [+] IT] _[_' 16 13 --32"430607
SLA1 ['] [C] _ 34 16 --32"388193
YFR024C [-] [U] _ ! 20
16
CCT3 [+] [F] _" CCT2 [+] IF] _ 24 14 "32"080316
51
YGR090W [+] [U]
PWP2 [+] [C] _1_" 57 23 --32'075322
SSF1[4 [C] _/i_ _ 26
YKR081C [+] [U] _" 45 18 --31"825822
I
18
YGL004C [-] [U] RPT1 [+] [F] _,r,_ 30 15 -31.845977
16
OFT2 [+] [T]
YSH1 [+] [T] _ 17 13 1.802497
115
TEM1 [+]
[D] I_ SRP1 [+][O] _ , 196 44 1-31.785039
16
SKI6 [+] IT]
RRP45 [+] IT] _ ' 18 13 -31.246473
T
CFT2 [+] [T] 16 t
PTA1 [+] [TJ _' _ 18 13 -31.246473
26
RPN8 [+] [F] _!_
RPN10 [-] [F] _t i 37 17 -31.169855
t
RPN8 [+] [FJ _t 26 RPN10 [-] IF] _' 3/ If i-3].]_g855
I
18
SNU71 [+] [FJ ' i LUC7 [+] [T] !1_1_ 23 14 1-31.055475
I .... [
42
RPN5 [+] [F] _ 54 21 1-30.988230
I RPT3 [+][F]
YGL161C [-J [U] 19 YGL198W [-] [U] 22 14 -30.883548
CFT2 [+] [T] 16 PAP1 [+] [T] '_II_I_LC'r_ 19 13 -30.746150
REF2 [-] [T] _ _[I_' 17 PTA1 [+] [1-] 18 13 -30.618549
25
ROX3 [-] [B] ._z, MED7 [+] [B] _i_'_' 32 16 -30.334202
i
27
CKB1 [-] [T] '-_[_ CKA1 [-] IT] _ _ 65 19 -30.252221
I
CFT1 [+] [T] _ 14 16
YKL059C [+] [U] _
t
12 _.151475
CFT1 [+] [T] _:' 14 16
CFT2 [+] [T] | 12 1-30.151475
I i7 |
YIF1 [+] [O] YGL161C [-] [U] _ ' 19 t3 1-30.1183i9
BET1 [+] [O] _ 19 BOS1 [+] [0] _ 24
14 1-30.096782
GALl 1 [-] [T] _I_-[ SRB6 [+] [T] _ 30 15 -30.027344
i
18
YGL004C [-] [U] _ i RPN12 [+] IF] _J" 26 14 -29.984041
RPN11 [+] [F] 23 RPN10 [-] IF] 37
l 16 -29.924467 .... i
YGL004C [-] [U] 18 RPT3 [+] IF] 54 16 -29.908208
14
RPT2 [+] IF] _" RPN3 [+] IF] 17 12 -29.620182
|
PTA1 [+J [T] :_ 18 PAP1 [+] IT] , 19 13 -29.562574
YNL110C [+] [U] _J_" 30 NOP2 [+] IT] _i, 48 18 -29.496631
YKR081C [+] [U] 45 CDC95 [+] [P] _D'_ 48 20 -29.364174
RPN11 [+] IF] 23 RPT3 [+] IF] 54
17 1-29.192525
YHC1 [+] [T] _ 14 SNU71 [+] IT] 18 12 -29.143247
CFT1 [+] [-I-] 14 PTA1 [+] [T] 18 12 -29.143247
RPN9 [+] [F] _" 21 RPT6 [+] IF] _ ! 24 14 -29.098643
RPN9 [+] IF) _ 21 RPT6 [+] [F] _ 24 14 -29.098643
38
NOP4 [+] [TJ
NOP2 [+] IT] _ 48 19 L-29,095719
RPNll [+] IF] _
23 RPT1 [+] IF] _1_ _ 30 _5 -29.074176
23
RPN11 [+] IF]
RPN6[+][F] _! 30 15 -29.074176
27
YHR052W [-] [U] _lr _ 34 16 -28.970022
YGR103W [+] [U] i.
15
GtCI [-] [C] _ GIC2 [-] [C] 17 12 -28.921676
_i
16
SKI6 [+] IT] _'1It_! RRP46 [+] IT] _' 16 12 -28.851188
16
DIS3 [+] [T] _: 16 12 1-28 851188
RRP46 [+] [T] _'
-- i -- J "
18
YGL004C [-] [U] '_
RPN6 [+] IF] '_
!
-I
NOP2 [+] [T] S I_ 8.64 44 !
26
RPN12 [+] [F] .." RPN10 [-] [F] _
16
YKL059C [+] [U] _ YSH1 [+] IT] _"qli__'i' 17 12 -28.320081
16
CFT2 [+] [TJ _ REF2 [-] IT] 17 12 -28.320081
22
PRP45 [+] [TJ '_ CEF1[+][DJ_ 25 14
1-28.3o 4391
35
MRP4 [-] [P] MRPS5 [-] |P] - 36 17 -28.290113 |
17
YDR036C [-] [U] MRP4 [-J[p] _ 35 14 -28.258046
33
NUP100 [-] [O] NUP57 [+] [O] 41_, 39 17 -28.107497
18 i
SPP381 [+.1][TJ SMX2 [-] IT] _'. 33 14 -28.058341
t7
YDR036C [-] [U] _ MRPS5 [-] [P] 36 14 -28.044447
23
YSC84 [-] [U] SLA1 [-] [C] _ 34 I 15 -27.999251
1
14
RPT2 [+] [F] _' RPN9 [+] [F] _-_ 21 , 12 !-27.944232
31
16
"27.888851 !
RPN_2[+][F] 26 15
-27-880880 1
RPN12[+][FJ _
RPT1 [+] [FJ _'
YKL059C[+][U]:'_ 16
PTA1 [+] [T] _'! 18 12 -27.843331
CFT2[+][_ 16 PFS2 [+] IT] _ 18 12 -27.843331
RRP46[+][T] 16
RRP45 [+] IT] _.[! 18 12 -27.843331
RPN12[+]IF] 26
'_ RPT3 [+] [F] _'_' 54 17 -27.712199,
18
YGL004C [-] [U] PREI I+]IF; _, 35 14 -27.606789
38
NOP4 [+] [T] YKR081C [+] [U] _ 45 t8 -27.553804
26
RPN12 [+] [F] r_ RPN5 [+] [F] _ 42 16 -27.487552
25
NUP49 [+] [O] _ NUP100 [-] [O] _ 33 15 -27.430676
YKL059C [+] [U] _l_t 16 PAP1 [+] [T] _ 19 12 -27.410048
REF2 [-] [T] '_! !7 18 12 -27 312410
FIP1 [+] [T]
YSHI14m 17
18 12 -27.312410
PTA1 [+] [T] -'Ib ''_
I
I 0DC27 [+] [D] _ 11 APCl [+] [D] _ 12 10 -27.288898
UBP6 [-] IF) 14 RPN10 [-] [F] _[ 37 13 -27.230502
...... I
17
YSHI [+] IT] 19 12 -26.879219
PAP1 [+] [T]
18
PTA1 [+] [T] 18 12 -26.835847
PFS2 [+] [T]
I _GALl1 [-] IT] _ 21 32 14 -26.722973
MED7 [+J [B]
, j ,,
/ "
PRP19 [+] [T] 16 21
CLF1 [+1[O]
1-26.6448751
"'I
MRPL10 [-] [P] _ 28 MRPL9 [-] [P] _ 32 15 -26.638762 I
i ....
RPN12 [+] IF] _t 26 PRE_[+][F] 35 15 -26.565064
YGR103W [+] [U] _! 34 YKR081C [+] [U] _ I-- 45 J 17 -26.48...3.213 i
..... ,...... ,.....
17
RPN3 [+] [F] 30 13 -26.477585
NOG t [+] [U] _r_ 27 l YGRRP1N036W[+][+[F]][U'_] _- 34 I 15 -26.456665
t
14
RPT2 [+] IF] RPN8 [+] [F] _" 26 12 -26.428532
RPT2[+][FJ_! 14
RPN8 [+] IF] "_"! t 26 12 -26.428532 i
J J l
FIP1[+]IT] 18
'I_ 19 12
PAP1[+] IT]
L
i-26.4027491
14
UBP6 [-] [F] _'_ RPN5 [+] [F] _ 42 13 -26,37586 !
t
23
RPN11 [+] IF] RPN5 [+] [F] 42 15 -26.27960_
18
[U] RPN5 [+] [F] _! 42 -26.251755
_R_ 004c [-]
l I 24
T6 [+] [F] _I RPT3 [+] IF] 54 16 -26.247617
21
TCPI [+][F]_. CCT2 [+] IF] _ 24 13 -26.228519
22
NAM8 [-] [T] LUC7 [+] [T] 23 13 -26,179343
CFTI [+][T] REZF__ 17 11 -26.126677
CFT1 [+] IT] _ 17 i 11 -26.126677
1414 y_YSH1 [+]
--i
17
RPN3 [+J [F] :_' 12
IF] '-
._RPN9, [+]
21
GALl 1[-] [T] ROX3 [-] [B] _ 13
-25.910505_
21
CLF! [+] [D] CEF1 [+][D] 25 13 -25.91050
26
NOP4 [+] IT] _! 38 15 -25.89O228
CKA2 [4 [T] 22 CKA1 [-] IT] 65 16 -25.753033
15
RPC34 [+] [1-] _ 26 12
RPO31 [+J [T]
-25.730864
UBP6 [-] IF] '_1_ _' YGL004C [-] [U] _ 18 11
-25.716782
f 1144
YTH1 [+] [r] PTA1 [+] IT] 18 11 -25.716782
14
CFT1 [+] IT] PFS2 [+]IT] '_1_ t 18 11 -25,716782
25
NGG1 [-] [B] ADA2 [-] [B] _ 3O 14 -25.654844;
21
FGALl 1 [-] IT] MED2 [-] [T] _ 26 13 -25.610220
22
LSM7 [-] [T] _ LSM5 [+] IT] 35 P 14 -25.595498
19
BET1 [+] [0] SEC22 [-] [OJ _ 2O 12 -25,572455
10
10 -25.479218