PROJECT #18425 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, 27 January 2023 12:14:44

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Project
Model Name
Folding@Home Identifier
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GPU
Model
PPD
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PROJECT FOLDING PPD AVERAGES BY CPU BETA

PPDDB data as of Friday, 27 January 2023 12:14:44

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 XEON CPU E5-2620 0 @ 2.00GHZ 12 4,661,813 55,941,756 Intel
2 RYZEN THREADRIPPER 2950X 16-CORE 32 1,553,143 49,700,576 AMD
3 RYZEN 7 5800X3D 8-CORE 16 60,152 962,432 AMD
4 RYZEN 9 7950X 16-CORE 32 27,396 876,672 AMD
5 RYZEN 9 5950X 16-CORE 32 22,933 733,856 AMD
6 RYZEN 7 7700X 8-CORE 16 38,202 611,232 AMD
7 CORE I9-10850K CPU @ 3.60GHZ 20 25,944 518,880 Intel
8 12TH GEN CORE I9-12900K 24 21,374 512,976 Intel
9 RYZEN 7 5700X 8-CORE 16 30,502 488,032 AMD
10 RYZEN 7 5800X 8-CORE 16 29,281 468,496 AMD
11 RYZEN 5 5500U 12 38,206 458,472 AMD
12 12TH GEN CORE I7-12700 20 22,762 455,240 Intel
13 RYZEN 9 3900 12-CORE 24 18,659 447,816 AMD
14 RYZEN THREADRIPPER 2970WX 24-CORE 48 9,253 444,144 AMD
15 RYZEN 9 3950X 16-CORE 32 13,599 435,168 AMD
16 12TH GEN CORE I7-12700K 20 21,558 431,160 Intel
17 11TH GEN CORE I7-11700K @ 3.60GHZ 16 26,581 425,296 Intel
18 RYZEN 9 3900XT 12-CORE 24 15,831 379,944 AMD
19 12TH GEN CORE I5-12600KF 16 22,923 366,768 Intel
20 12TH GEN CORE I5-12600K 16 22,722 363,552 Intel
21 XEON CPU E5-2690 V4 @ 2.60GHZ 28 12,376 346,528 Intel
22 RYZEN 9 3900X 12-CORE 24 13,990 335,760 AMD
23 11TH GEN CORE I9-11900K @ 3.50GHZ 16 20,895 334,320 Intel
24 12TH GEN CORE I5-12400 12 27,561 330,732 Intel
25 CORE I9-9900K CPU @ 3.60GHZ 16 19,402 310,432 Intel
26 RYZEN 9 5900X 12-CORE 24 12,914 309,936 AMD
27 XEON CPU E5-2680 V2 @ 2.80GHZ 40 7,594 303,760 Intel
28 RYZEN 7 3800X 8-CORE 16 18,822 301,152 AMD
29 RYZEN 5 5600X 6-CORE 12 21,515 258,180 AMD
30 RYZEN 5 PRO 5650G 12 20,345 244,140 AMD
31 CORE I9-10900X CPU @ 3.70GHZ 20 11,942 238,840 Intel
32 RYZEN 7 5800H 16 14,556 232,896 AMD
33 CORE I7-10700K CPU @ 3.80GHZ 16 14,317 229,072 Intel
34 12TH GEN CORE I9-12900H 20 11,416 228,320 Intel
35 XEON CPU E5-2680 V3 @ 2.50GHZ 24 9,485 227,640 Intel
36 CORE I7-8700 CPU @ 3.20GHZ 12 18,900 226,800 Intel
37 RYZEN 5 5600G 12 18,637 223,644 AMD
38 XEON CPU E5-2660 V3 @ 2.60GHZ 20 10,744 214,880 Intel
39 CORE I5-10400 CPU @ 2.90GHZ 12 17,279 207,348 Intel
40 RYZEN 5 3600 6-CORE 12 15,497 185,964 AMD
41 XEON CPU X5660 @ 2.80GHZ 24 7,351 176,424 Intel
42 RYZEN 7 5700G 16 11,012 176,192 AMD
43 XEON CPU E5-2670 0 @ 2.60GHZ 32 5,500 176,000 Intel
44 RYZEN 7 PRO 4750G 16 10,841 173,456 AMD
45 RYZEN 7 3700X 8-CORE 16 9,904 158,464 AMD
46 XEON CPU E5-2698 V4 @ 2.20GHZ 16 9,851 157,616 Intel
47 CORE I7-10700 CPU @ 2.90GHZ 16 8,931 142,896 Intel
48 RYZEN 7 1700 EIGHT-CORE 16 8,795 140,720 AMD
49 11TH GEN CORE I5-11400 @ 2.60GHZ 12 10,176 122,112 Intel
50 CORE I7-10750H CPU @ 2.60GHZ 12 9,929 119,148 Intel
51 CORE I7-10700T CPU @ 2.00GHZ 16 7,197 115,152 Intel
52 CORE I9-8950HK CPU @ 2.90GHZ 12 8,089 97,068 Intel
53 RYZEN 7 2700X EIGHT-CORE 16 6,022 96,352 AMD
54 APPLE M1 PRO 10 7,497 74,970 Apple
55 XEON CPU E5-2680 0 @ 2.70GHZ 16 3,915 62,640 Intel
56 XEON CPU E5-2450 0 @ 2.10GHZ 10 6,100 61,000 Intel
57 CORE I7-8750H CPU @ 2.20GHZ 12 3,183 38,196 Intel