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: GRO_A8

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

PPDDB data as of Tuesday, 27 September 2022 13:39:56

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

PPDDB data as of Tuesday, 27 September 2022 13:39:56

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 CORE I7-8700 CPU @ 3.20GHZ 12 143,235 1,718,820 Intel
2 11TH GEN CORE I5-11400F @ 2.60GHZ 12 60,307 723,684 Intel
3 12TH GEN CORE I9-12900K 24 23,839 572,136 Intel
4 EPYC 7V12 64-CORE 64 8,681 555,584 AMD
5 RYZEN 9 5950X 16-CORE 32 16,846 539,072 AMD
6 11TH GEN CORE I9-11900K @ 3.50GHZ 16 30,360 485,760 Intel
7 RYZEN 7 5800X 8-CORE 16 30,313 485,008 AMD
8 RYZEN 9 3950X 16-CORE 32 14,886 476,352 AMD
9 RYZEN 7 5700X 8-CORE 16 27,557 440,912 AMD
10 XEON CPU E5-2690 V4 @ 2.60GHZ 28 15,027 420,756 Intel
11 RYZEN 9 3900 12-CORE 24 17,468 419,232 AMD
12 11TH GEN CORE I7-11700K @ 3.60GHZ 16 26,136 418,176 Intel
13 RYZEN 7 5700G 16 25,488 407,808 AMD
14 12TH GEN CORE I7-12700 20 19,849 396,980 Intel
15 RYZEN 9 3900X 12-CORE 24 14,772 354,528 AMD
16 CORE I5-9600K CPU @ 3.70GHZ 6 57,209 343,254 Intel
17 RYZEN 7 3800X 8-CORE 16 21,287 340,592 AMD
18 CORE I7-10700K CPU @ 3.80GHZ 16 20,813 333,008 Intel
19 XEON W-1290P CPU @ 3.70GHZ 20 16,426 328,520 Intel
20 CORE I9-9900K CPU @ 3.60GHZ 16 15,784 252,544 Intel
21 XEON CPU E5-2650 V2 @ 2.60GHZ 32 7,561 241,952 Intel
22 CORE I7-5960X CPU @ 3.00GHZ 16 14,868 237,888 Intel
23 CORE I9-10900X CPU @ 3.70GHZ 20 11,866 237,320 Intel
24 RYZEN 5 5600X 6-CORE 12 19,481 233,772 AMD
25 XEON CPU E5-2680 V3 @ 2.50GHZ 24 9,195 220,680 Intel
26 12TH GEN CORE I7-12700K 20 9,595 191,900 Intel
27 XEON GOLD 6128 CPU @ 3.40GHZ 12 14,830 177,960 Intel
28 CORE I5-10400 CPU @ 2.90GHZ 12 14,019 168,228 Intel
29 11TH GEN CORE I9-11900F @ 2.50GHZ 16 10,498 167,968 Intel
30 RYZEN 7 PRO 4750G 16 10,293 164,688 AMD
31 CORE I7-10700 CPU @ 2.90GHZ 16 9,740 155,840 Intel
32 RYZEN 5 3600 6-CORE 12 12,183 146,196 AMD
33 XEON CPU E5-2698 V4 @ 2.20GHZ 16 8,962 143,392 Intel
34 11TH GEN CORE I5-11400 @ 2.60GHZ 12 11,494 137,928 Intel
35 RYZEN 7 3700X 8-CORE 16 8,350 133,600 AMD
36 CORE I7-8700K CPU @ 3.70GHZ 12 10,835 130,020 Intel
37 CORE I7-10700T CPU @ 2.00GHZ 16 7,812 124,992 Intel
38 CORE I9-8950HK CPU @ 2.90GHZ 12 9,559 114,708 Intel
39 RYZEN 5 1600 SIX-CORE 12 9,308 111,696 AMD
40 RYZEN 9 5900HX 16 6,749 107,984 AMD
41 CORE I7-5820K CPU @ 3.30GHZ 12 8,919 107,028 Intel
42 RYZEN 5 2600 SIX-CORE 12 8,786 105,432 AMD
43 XEON CPU E5-2680 0 @ 2.70GHZ 16 5,851 93,616 Intel
44 XEON CPU E5-2450 0 @ 2.10GHZ 10 6,224 62,240 Intel