PROJECT #18421 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: 80,500

Core: 0xa8

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

PPDDB data as of Friday, 03 February 2023 06:15:10

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 Friday, 03 February 2023 06:15:10

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 RYZEN 5 2600 SIX-CORE 12 357,157 4,285,884 AMD
2 13TH GEN CORE I9-13900KS 32 34,151 1,092,832 Intel
3 RYZEN 9 7950X 16-CORE 32 28,410 909,120 AMD
4 RYZEN 5 5600G 12 60,898 730,776 AMD
5 RYZEN 7 7700X 8-CORE 16 40,245 643,920 AMD
6 12TH GEN CORE I7-12700K 20 30,355 607,100 Intel
7 RYZEN 9 5950X 16-CORE 32 17,325 554,400 AMD
8 12TH GEN CORE I9-12900K 24 22,950 550,800 Intel
9 RYZEN 9 5900X 12-CORE 24 20,756 498,144 AMD
10 RYZEN 7 5700X 8-CORE 16 29,838 477,408 AMD
11 RYZEN 9 3900 12-CORE 24 19,438 466,512 AMD
12 12TH GEN CORE I7-12700 20 22,465 449,300 Intel
13 RYZEN 7 5800X 8-CORE 16 26,028 416,448 AMD
14 RYZEN 7 5800X3D 8-CORE 16 25,632 410,112 AMD
15 11TH GEN CORE I7-11700K @ 3.60GHZ 16 25,451 407,216 Intel
16 CORE I9-10900K CPU @ 3.70GHZ 20 19,355 387,100 Intel
17 CORE I9-7920X CPU @ 2.90GHZ 24 15,074 361,776 Intel
18 RYZEN 9 3900XT 12-CORE 24 15,053 361,272 AMD
19 CORE I9-10850K CPU @ 3.60GHZ 20 17,092 341,840 Intel
20 RYZEN 9 3950X 16-CORE 32 10,659 341,088 AMD
21 XEON CPU E5-2690 V4 @ 2.60GHZ 28 12,093 338,604 Intel
22 12TH GEN CORE I5-12400 12 27,966 335,592 Intel
23 RYZEN 9 3900X 12-CORE 24 13,037 312,888 AMD
24 RYZEN 7 3800X 8-CORE 16 19,358 309,728 AMD
25 EPYC 7401P 24-CORE 48 6,450 309,600 AMD
26 11TH GEN CORE I5-11400F @ 2.60GHZ 12 25,316 303,792 Intel
27 11TH GEN CORE I5-11600K @ 3.90GHZ 12 24,897 298,764 Intel
28 11TH GEN CORE I9-11900K @ 3.50GHZ 16 18,000 288,000 Intel
29 XEON CPU E5-2680 V3 @ 2.50GHZ 24 10,632 255,168 Intel
30 RYZEN 5 PRO 5650G 12 20,882 250,584 AMD
31 RYZEN 7 5700G 16 15,314 245,024 AMD
32 RYZEN 9 5900 12-CORE 24 10,056 241,344 AMD
33 CORE I9-9900 CPU @ 3.10GHZ 16 14,965 239,440 Intel
34 CORE I7-8700 CPU @ 3.20GHZ 12 18,648 223,776 Intel
35 CORE I9-7940X CPU @ 3.10GHZ 28 7,949 222,572 Intel
36 RYZEN 5 5600X 6-CORE 12 17,808 213,696 AMD
37 RYZEN 5 3600 6-CORE 12 17,387 208,644 AMD
38 CORE I9-9900K CPU @ 3.60GHZ 16 12,433 198,928 Intel
39 CORE I9-8950HK CPU @ 2.90GHZ 12 16,056 192,672 Intel
40 RYZEN 7 3700X 8-CORE 16 10,971 175,536 AMD
41 CORE I5-10400 CPU @ 2.90GHZ 12 14,311 171,732 Intel
42 CORE I9-9900KF CPU @ 3.60GHZ 16 10,481 167,696 Intel
43 RYZEN 7 PRO 4750G 16 10,098 161,568 AMD
44 CORE I7-10700 CPU @ 2.90GHZ 16 9,542 152,672 Intel
45 XEON CPU E5-2698 V4 @ 2.20GHZ 16 8,772 140,352 Intel
46 CORE I7-5820K CPU @ 3.30GHZ 12 11,545 138,540 Intel
47 11TH GEN CORE I5-11400 @ 2.60GHZ 12 10,986 131,832 Intel
48 CORE I7-9750H CPU @ 2.60GHZ 12 10,808 129,696 Intel
49 CORE I7-10700T CPU @ 2.00GHZ 16 7,631 122,096 Intel
50 CORE I5-10400F CPU @ 2.90GHZ 12 9,682 116,184 Intel
51 RYZEN 5 1600 SIX-CORE 12 9,390 112,680 AMD
52 RYZEN 7 2700X EIGHT-CORE 16 7,012 112,192 AMD
53 XEON CPU E5-2620 V3 @ 2.40GHZ 12 8,417 101,004 Intel
54 RYZEN 9 5900HS 16 6,238 99,808 AMD
55 RYZEN 5 2600X SIX-CORE 12 8,303 99,636 AMD
56 XEON CPU E5-2697 V2 @ 2.70GHZ 24 3,891 93,384 Intel
57 APPLE M1 PRO 10 6,782 67,820 Apple
58 XEON CPU E5-2680 0 @ 2.70GHZ 16 3,878 62,048 Intel
59 XEON CPU E5-2620 0 @ 2.00GHZ 12 2,965 35,580 Intel