PROJECT #18423 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 Monday, 03 October 2022 12:16:28

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 Monday, 03 October 2022 12:16:28

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 CORE I9-8950HK CPU @ 2.90GHZ 12 155,072 1,860,864 Intel
2 12TH GEN CORE I7-12700K 20 29,870 597,400 Intel
3 12TH GEN CORE I9-12900K 24 22,132 531,168 Intel
4 RYZEN 9 3950X 16-CORE 32 16,197 518,304 AMD
5 CORE I7-8700 CPU @ 3.20GHZ 12 42,146 505,752 Intel
6 RYZEN 9 5900X 12-CORE 24 20,371 488,904 AMD
7 RYZEN 9 5950X 16-CORE 32 14,860 475,520 AMD
8 RYZEN 7 5700X 8-CORE 16 29,560 472,960 AMD
9 RYZEN 9 3900 12-CORE 24 18,000 432,000 AMD
10 11TH GEN CORE I7-11700K @ 3.60GHZ 16 26,334 421,344 Intel
11 RYZEN 7 5800X 8-CORE 16 26,068 417,088 AMD
12 CORE I7-10870H CPU @ 2.20GHZ 16 23,738 379,808 Intel
13 RYZEN 7 5700G 16 23,260 372,160 AMD
14 12TH GEN CORE I7-12700 20 17,776 355,520 Intel
15 RYZEN 7 5800X3D 8-CORE 16 22,044 352,704 AMD
16 CORE I9-7920X CPU @ 2.90GHZ 24 14,222 341,328 Intel
17 EPYC 7401P 24-CORE 48 7,102 340,896 AMD
18 XEON CPU E5-2690 V4 @ 2.60GHZ 28 11,999 335,972 Intel
19 11TH GEN CORE I5-11600K @ 3.90GHZ 12 27,458 329,496 Intel
20 RYZEN 9 3900X 12-CORE 24 13,242 317,808 AMD
21 RYZEN THREADRIPPER 2970WX 24-CORE 48 6,536 313,728 AMD
22 CORE I9-10850K CPU @ 3.60GHZ 20 15,676 313,520 Intel
23 RYZEN 7 3800X 8-CORE 16 19,427 310,832 AMD
24 CORE I7-10700T CPU @ 2.00GHZ 16 17,584 281,344 Intel
25 CORE I9-9900K CPU @ 3.60GHZ 16 16,289 260,624 Intel
26 CORE I9-10900X CPU @ 3.70GHZ 20 12,499 249,980 Intel
27 RYZEN 5 3600 6-CORE 12 20,699 248,388 AMD
28 XEON CPU E5-2680 V3 @ 2.50GHZ 24 10,116 242,784 Intel
29 EPYC 7V12 64-CORE 64 3,659 234,176 AMD
30 RYZEN 5 5600X 6-CORE 12 19,117 229,404 AMD
31 CORE I9-9900X CPU @ 3.50GHZ 20 11,234 224,680 Intel
32 XEON CPU E5-2680 V2 @ 2.80GHZ 40 5,469 218,760 Intel
33 CORE I5-10600 CPU @ 3.30GHZ 12 17,294 207,528 Intel
34 XEON CPU E5-2650 V2 @ 2.60GHZ 32 6,102 195,264 Intel
35 RYZEN 7 PRO 4750G 16 11,787 188,592 AMD
36 RYZEN 7 2700X EIGHT-CORE 16 11,468 183,488 AMD
37 CORE I7-10700K CPU @ 3.80GHZ 16 11,430 182,880 Intel
38 CORE I5-10400 CPU @ 2.90GHZ 12 14,628 175,536 Intel
39 11TH GEN CORE I9-11900F @ 2.50GHZ 16 10,179 162,864 Intel
40 XEON CPU E5-2698 V4 @ 2.20GHZ 16 9,997 159,952 Intel
41 CORE I7-9750H CPU @ 2.60GHZ 12 13,172 158,064 Intel
42 RYZEN 7 3700X 8-CORE 16 9,719 155,504 AMD
43 RYZEN 7 1800X EIGHT-CORE 16 9,446 151,136 AMD
44 RYZEN 5 2600 SIX-CORE 12 11,248 134,976 AMD
45 CORE I7-10700 CPU @ 2.90GHZ 16 8,189 131,024 Intel
46 XEON GOLD 6128 CPU @ 3.40GHZ 12 10,830 129,960 Intel
47 RYZEN 5 1600 SIX-CORE 12 9,298 111,576 AMD
48 11TH GEN CORE I5-11400 @ 2.60GHZ 12 8,966 107,592 Intel
49 XEON CPU E5-2680 0 @ 2.70GHZ 16 5,737 91,792 Intel
50 CORE I7-8850H CPU @ 2.60GHZ 12 4,159 49,908 Intel
51 XEON CPU E5-2620 0 @ 2.00GHZ 12 3,815 45,780 Intel
52 XEON CPU E5-2697 V2 @ 2.70GHZ 24 1,608 38,592 Intel