PROJECT #18424 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 Tuesday, 07 February 2023 12:14:54

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 Tuesday, 07 February 2023 12:14:54

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 XEON CPU X5660 @ 2.80GHZ 24 351,770 8,442,480 Intel
2 CORE I7-8700 CPU @ 3.20GHZ 12 143,065 1,716,780 Intel
3 13TH GEN CORE I9-13900KS 32 33,818 1,082,176 Intel
4 RYZEN 9 7950X 16-CORE 32 27,533 881,056 AMD
5 11TH GEN CORE I5-11400F @ 2.60GHZ 12 60,307 723,684 Intel
6 RYZEN 7 7700X 8-CORE 16 42,181 674,896 AMD
7 RYZEN 9 5950X 16-CORE 32 19,805 633,760 AMD
8 12TH GEN CORE I9-12900K 24 23,839 572,136 Intel
9 RYZEN 7 5800X3D 8-CORE 16 35,637 570,192 AMD
10 EPYC 7V12 64-CORE 64 8,681 555,584 AMD
11 RYZEN 7 5800X 8-CORE 16 34,221 547,536 AMD
12 RYZEN 9 5900X 12-CORE 24 21,192 508,608 AMD
13 RYZEN 9 3950X 16-CORE 32 14,886 476,352 AMD
14 RYZEN 7 5700X 8-CORE 16 29,224 467,584 AMD
15 RYZEN 9 3900XT 12-CORE 24 19,067 457,608 AMD
16 XEON CPU E5-2690 V4 @ 2.60GHZ 28 15,027 420,756 Intel
17 RYZEN 9 3900 12-CORE 24 17,468 419,232 AMD
18 11TH GEN CORE I7-11700K @ 3.60GHZ 16 26,136 418,176 Intel
19 12TH GEN CORE I7-12700 20 19,849 396,980 Intel
20 11TH GEN CORE I9-11900K @ 3.50GHZ 16 23,485 375,760 Intel
21 CORE I5-9600K CPU @ 3.70GHZ 6 57,209 343,254 Intel
22 XEON W-1290P CPU @ 3.70GHZ 20 16,426 328,520 Intel
23 RYZEN 7 3800X 8-CORE 16 20,529 328,464 AMD
24 12TH GEN CORE I5-12400 12 26,502 318,024 Intel
25 RYZEN 9 3900X 12-CORE 24 12,906 309,744 AMD
26 CORE I7-10700K CPU @ 3.80GHZ 16 19,139 306,224 Intel
27 RYZEN 9 5900 12-CORE 24 11,117 266,808 AMD
28 RYZEN 5 PRO 5650G 12 21,534 258,408 AMD
29 RYZEN 7 5700G 16 15,767 252,272 AMD
30 RYZEN 7 5800H 16 15,686 250,976 AMD
31 CORE I7-5960X CPU @ 3.00GHZ 16 14,868 237,888 Intel
32 CORE I9-10900X CPU @ 3.70GHZ 20 11,866 237,320 Intel
33 RYZEN 5 5600X 6-CORE 12 19,319 231,828 AMD
34 XEON CPU E5-2680 V3 @ 2.50GHZ 24 9,195 220,680 Intel
35 RYZEN 5 5600G 12 18,361 220,332 AMD
36 CORE I9-9900K CPU @ 3.60GHZ 16 13,234 211,744 Intel
37 12TH GEN CORE I7-12700K 20 10,366 207,320 Intel
38 XEON CPU E5-2650 V2 @ 2.60GHZ 32 6,321 202,272 Intel
39 RYZEN 5 3600 6-CORE 12 16,090 193,080 AMD
40 XEON GOLD 6128 CPU @ 3.40GHZ 12 14,830 177,960 Intel
41 RYZEN 7 3700X 8-CORE 16 10,943 175,088 AMD
42 RYZEN 7 PRO 4750G 16 10,749 171,984 AMD
43 11TH GEN CORE I9-11900F @ 2.50GHZ 16 10,498 167,968 Intel
44 CORE I5-10400 CPU @ 2.90GHZ 12 13,779 165,348 Intel
45 CORE I7-5930K CPU @ 3.50GHZ 12 13,670 164,040 Intel
46 11TH GEN CORE I5-11400 @ 2.60GHZ 12 13,304 159,648 Intel
47 CORE I7-10700 CPU @ 2.90GHZ 16 9,740 155,840 Intel
48 XEON CPU E5-2670 0 @ 2.60GHZ 32 4,675 149,600 Intel
49 CORE I7-5820K CPU @ 3.30GHZ 12 12,181 146,172 Intel
50 XEON CPU E5-2698 V4 @ 2.20GHZ 16 8,962 143,392 Intel
51 CORE I7-8700K CPU @ 3.70GHZ 12 10,835 130,020 Intel
52 CORE I9-8950HK CPU @ 2.90GHZ 12 9,559 114,708 Intel
53 CORE I7-10700T CPU @ 2.00GHZ 16 7,024 112,384 Intel
54 RYZEN 5 1600 SIX-CORE 12 9,308 111,696 AMD
55 RYZEN 9 5900HX 16 6,749 107,984 AMD
56 RYZEN 5 2600 SIX-CORE 12 8,786 105,432 AMD
57 XEON CPU E5-2680 0 @ 2.70GHZ 16 5,851 93,616 Intel
58 APPLE M1 PRO 10 7,831 78,310 Apple
59 XEON CPU E5-2697 V2 @ 2.70GHZ 24 2,831 67,944 Intel
60 XEON CPU E5-2450 0 @ 2.10GHZ 10 6,224 62,240 Intel
61 RYZEN 5 5500U 12 3,254 39,048 AMD