PROJECT #18405 RESEARCH FOR CANCER
FOLDING PERFORMANCE PROFILE

PROJECT SUMMARY

Can molecular simulation be used for virtual affinity-maturation of de novo designed protein binders? That’s the question this project aims to address.

The Bahl Lab at the Institute for Protein Innovation has had some amazing success using computational design to develop high-affinity mini-proteins that can inhibit protein targets by tightly binding to them.

In practice, the current approach requires the experimental screening of thousands of computational designs to discover a few tight binders, and similarly expensive experimental screens to optimize their binding (i.e.

“affinity maturation”).

If we can make more accurate predictions of how sequence mutations affect binding affinity, we may be able to offload this expensive task to computers, boosting the efficiency of these efforts considerably. In this project, we use relative free energy calculations to predict how single-point mutations of a computationally designed mini-protein alter the binding affinity to the periplasmic protease LapG, an important regulator of bacterial biofilm formation.

These predictions will be compared to high-throughput experimental measurements of binding affinity provided by the Bahl lab.

An important end goal of this work is to develop new classes of inhibitors to make antibiotic therapies more successful.

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PROJECT INFO

Manager(s): Prof. Vincent Voelz

Institution: Temple University

PROJECT WORK UNIT SUMMARY

Atoms: 24,700

Core: 0xa8

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

PPDDB data as of Wednesday, 07 December 2022 06:13:22

Rank
Project
Model Name
Folding@Home Identifier
Make
Brand
GPU
Model
PPD
Average
Points WU
Average
WUs Day
Average
WU Time
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PROJECT FOLDING PPD AVERAGES BY CPU BETA

PPDDB data as of Wednesday, 07 December 2022 06:13:22

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 CORE I9-8950HK CPU @ 2.90GHZ 12 135,615 1,627,380 Intel
2 RYZEN 9 3950X 16-CORE 32 34,263 1,096,416 AMD
3 RYZEN 7 5800X3D 8-CORE 16 50,041 800,656 AMD
4 RYZEN 9 5950X 16-CORE 32 24,990 799,680 AMD
5 RYZEN 7 5800X 8-CORE 16 45,471 727,536 AMD
6 RYZEN 7 7700X 8-CORE 16 39,974 639,584 AMD
7 RYZEN 9 5900X 12-CORE 24 25,049 601,176 AMD
8 RYZEN 7 5700G 16 37,010 592,160 AMD
9 12TH GEN CORE I7-12700K 20 27,411 548,220 Intel
10 12TH GEN CORE I9-12900K 24 21,375 513,000 Intel
11 RYZEN 7 5700X 8-CORE 16 27,829 445,264 AMD
12 11TH GEN CORE I7-11700K @ 3.60GHZ 16 26,235 419,760 Intel
13 11TH GEN CORE I9-11900K @ 3.50GHZ 16 25,883 414,128 Intel
14 RYZEN THREADRIPPER 1950X 16-CORE 32 12,191 390,112 AMD
15 RYZEN 9 3900 12-CORE 24 15,811 379,464 AMD
16 EPYC 7V12 64-CORE 64 5,751 368,064 AMD
17 RYZEN 9 3900XT 12-CORE 24 14,409 345,816 AMD
18 RYZEN 7 3800X 8-CORE 16 21,065 337,040 AMD
19 CORE I9-10900X CPU @ 3.70GHZ 20 16,056 321,120 Intel
20 CORE I9-10850K CPU @ 3.60GHZ 20 15,009 300,180 Intel
21 CORE I9-9900K CPU @ 3.60GHZ 16 18,239 291,824 Intel
22 RYZEN 9 3900X 12-CORE 24 10,256 246,144 AMD
23 RYZEN 9 5900HS 16 14,982 239,712 AMD
24 RYZEN 5 5600X 6-CORE 12 19,922 239,064 AMD
25 RYZEN THREADRIPPER 3960X 24-CORE 48 4,849 232,752 AMD
26 XEON CPU E5-2680 V3 @ 2.50GHZ 24 9,218 221,232 Intel
27 XEON CPU E5-2680 V2 @ 2.80GHZ 40 5,519 220,760 Intel
28 APPLE M1 MAX 10 22,034 220,340 Apple
29 CORE I7-10700K CPU @ 3.80GHZ 16 13,491 215,856 Intel
30 RYZEN 5 2600X SIX-CORE 12 17,811 213,732 AMD
31 CORE I7-8700 CPU @ 3.20GHZ 12 17,055 204,660 Intel
32 RYZEN 7 5800H 16 12,407 198,512 AMD
33 RYZEN 7 3700X 8-CORE 16 12,299 196,784 AMD
34 RYZEN 5 5600G 12 16,327 195,924 AMD
35 RYZEN 7 PRO 4750G 16 11,814 189,024 AMD
36 12TH GEN CORE I3-12100F 8 23,213 185,704 Intel
37 RYZEN 5 3600 6-CORE 12 14,756 177,072 AMD
38 XEON CPU E5-2697 V2 @ 2.70GHZ 24 7,245 173,880 Intel
39 12TH GEN CORE I9-12900H 20 7,843 156,860 Intel
40 RYZEN THREADRIPPER 2950X 16-CORE 32 4,884 156,288 AMD
41 CORE I7-9700K CPU @ 3.60GHZ 8 19,366 154,928 Intel
42 XEON GOLD 6128 CPU @ 3.40GHZ 12 12,873 154,476 Intel
43 11TH GEN CORE I5-11400 @ 2.60GHZ 12 11,774 141,288 Intel
44 CORE I7-9700 CPU @ 3.00GHZ 8 17,277 138,216 Intel
45 RYZEN 9 4900HS 16 8,232 131,712 AMD
46 CORE I5-10400 CPU @ 2.90GHZ 12 10,822 129,864 Intel
47 CORE I7-7700K CPU @ 4.20GHZ 8 14,673 117,384 Intel
48 CORE I7-3770 CPU @ 3.40GHZ 8 13,986 111,888 Intel
49 RYZEN 5 3400G 8 13,440 107,520 AMD
50 CORE I7-7700 CPU @ 3.60GHZ 8 12,834 102,672 Intel
51 RYZEN 7 2700X EIGHT-CORE 16 6,223 99,568 AMD
52 CORE I7-10700T CPU @ 2.00GHZ 16 6,133 98,128 Intel
53 CORE I7-4790K CPU @ 4.00GHZ 8 11,649 93,192 Intel
54 RYZEN 5 1600 SIX-CORE 12 7,410 88,920 AMD
55 RYZEN 5 PRO 2400G 8 10,698 85,584 AMD
56 XEON CPU E3-1270 V5 @ 3.60GHZ 8 10,649 85,192 Intel
57 CORE I7-8705G CPU @ 3.10GHZ 8 10,114 80,912 Intel
58 11TH GEN CORE I9-11900F @ 2.50GHZ 16 4,900 78,400 Intel
59 CORE I7-9750H CPU @ 2.60GHZ 12 6,379 76,548 Intel
60 XEON CPU E5-1630 V3 @ 3.70GHZ 8 8,904 71,232 Intel
61 CORE I7-4770K CPU @ 3.50GHZ 8 8,570 68,560 Intel
62 XEON CPU E5-2680 0 @ 2.70GHZ 16 4,018 64,288 Intel
63 CORE I7-6700K CPU @ 4.00GHZ 8 7,888 63,104 Intel
64 XEON W-10855M CPU @ 2.80GHZ 12 4,690 56,280 Intel
65 CORE I7-4770HQ CPU @ 2.20GHZ 8 6,687 53,496 Intel
66 11TH GEN CORE I5-1145G7 @ 2.60GHZ 8 6,102 48,816 Intel
67 XEON CPU E3-1245 V2 @ 3.40GHZ 8 5,261 42,088 Intel
68 XEON CPU E31245 @ 3.30GHZ 8 4,774 38,192 Intel
69 XEON CPU E3-1240 V2 @ 3.40GHZ 8 4,433 35,464 Intel
70 11TH GEN CORE I7-1165G7 @ 2.80GHZ 8 4,432 35,456 Intel
71 CORE I7-3770K CPU @ 3.50GHZ 8 3,213 25,704 Intel
72 APPLE M1 8 2,632 21,056 Apple
73 CORE I5-8350U CPU @ 1.70GHZ 8 2,080 16,640 Intel