PROJECT #18409 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: 64,500

Core: 0xa8

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

PPDDB data as of Friday, 03 February 2023 06:15:11

Rank
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, 03 February 2023 06:15:11

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 13TH GEN CORE I9-13900KS 32 24,757 792,224 Intel
2 CORE I9-10850K CPU @ 3.60GHZ 20 36,403 728,060 Intel
3 RYZEN 9 5950X 16-CORE 32 18,514 592,448 AMD
4 RYZEN 7 7700X 8-CORE 16 37,002 592,032 AMD
5 RYZEN 7 5800X 8-CORE 16 35,742 571,872 AMD
6 12TH GEN CORE I9-12900K 24 22,428 538,272 Intel
7 RYZEN 9 3950X 16-CORE 32 14,958 478,656 AMD
8 RYZEN 9 3900 12-CORE 24 19,548 469,152 AMD
9 EPYC 7V12 64-CORE 64 7,178 459,392 AMD
10 12TH GEN CORE I7-12700K 20 22,562 451,240 Intel
11 RYZEN 7 5700X 8-CORE 16 25,257 404,112 AMD
12 11TH GEN CORE I7-11700K @ 3.60GHZ 16 24,500 392,000 Intel
13 RYZEN 9 5900X 12-CORE 24 15,962 383,088 AMD
14 RYZEN 9 3900XT 12-CORE 24 15,565 373,560 AMD
15 CORE I9-7920X CPU @ 2.90GHZ 24 15,282 366,768 Intel
16 12TH GEN CORE I7-12700 20 17,202 344,040 Intel
17 12TH GEN CORE I5-12400 12 26,565 318,780 Intel
18 CORE I9-7940X CPU @ 3.10GHZ 28 10,629 297,612 Intel
19 RYZEN 7 5700G 16 18,514 296,224 AMD
20 RYZEN 7 5800X3D 8-CORE 16 18,188 291,008 AMD
21 RYZEN 7 3800X 8-CORE 16 18,029 288,464 AMD
22 RYZEN 9 3900X 12-CORE 24 11,240 269,760 AMD
23 CORE I9-10900X CPU @ 3.70GHZ 20 13,481 269,620 Intel
24 RYZEN 5 3600 6-CORE 12 22,085 265,020 AMD
25 RYZEN 9 5900 12-CORE 24 10,729 257,496 AMD
26 CORE I9-9900X CPU @ 3.50GHZ 20 12,095 241,900 Intel
27 CORE I9-9900 CPU @ 3.10GHZ 16 14,721 235,536 Intel
28 XEON CPU E5-2680 V3 @ 2.50GHZ 24 9,428 226,272 Intel
29 12TH GEN CORE I9-12900H 20 11,276 225,520 Intel
30 XEON CPU E5-2650 V2 @ 2.60GHZ 32 6,958 222,656 Intel
31 11TH GEN CORE I9-11900K @ 3.50GHZ 16 13,799 220,784 Intel
32 CORE I9-9900K CPU @ 3.60GHZ 16 13,495 215,920 Intel
33 11TH GEN CORE I7-11850H @ 2.50GHZ 16 13,190 211,040 Intel
34 XEON CPU E5-2665 0 @ 2.40GHZ 32 6,276 200,832 Intel
35 RYZEN 7 PRO 4750G 16 12,125 194,000 AMD
36 12TH GEN CORE I5-12600K 16 12,034 192,544 Intel
37 11TH GEN CORE I5-11400F @ 2.60GHZ 12 14,262 171,144 Intel
38 11TH GEN CORE I9-11900F @ 2.50GHZ 16 10,385 166,160 Intel
39 RYZEN 7 3700X 8-CORE 16 10,218 163,488 AMD
40 CORE I7-10700T CPU @ 2.00GHZ 16 8,667 138,672 Intel
41 CORE I7-10870H CPU @ 2.20GHZ 16 8,399 134,384 Intel
42 XEON CPU E5-2690 V2 @ 3.00GHZ 20 6,453 129,060 Intel
43 11TH GEN CORE I7-11800H @ 2.30GHZ 16 8,065 129,040 Intel
44 CORE I7-6950X CPU @ 3.00GHZ 20 6,293 125,860 Intel
45 XEON CPU E5-2670 0 @ 2.60GHZ 32 3,545 113,440 Intel
46 CORE I9-9880H CPU @ 2.30GHZ 16 6,290 100,640 Intel
47 XEON CPU E5-2680 0 @ 2.70GHZ 16 6,181 98,896 Intel
48 RYZEN 7 4800H 16 6,046 96,736 AMD
49 RYZEN 7 2700X EIGHT-CORE 16 5,944 95,104 AMD
50 XEON CPU X5660 @ 2.80GHZ 24 3,375 81,000 Intel