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: 0xa8

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

PPDDB data as of Tuesday, 07 February 2023 06:14:50

Rank
Project
Model Name
Folding@Home Identifier
Make
Brand
GPU
Model
PPD
Average
Points WU
Average
WUs Day
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WU Time
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PROJECT FOLDING PPD AVERAGES BY CPU BETA

PPDDB data as of Tuesday, 07 February 2023 06:14:50

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 RYZEN 9 5950X 16-CORE 32 24,047 769,504 AMD
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 41,944 503,328 Intel
6 RYZEN 7 5800X3D 8-CORE 16 30,824 493,184 AMD
7 RYZEN 7 5700X 8-CORE 16 29,841 477,456 AMD
8 RYZEN 9 5900X 12-CORE 24 19,849 476,376 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 12TH GEN CORE I7-12700 20 17,776 355,520 Intel
14 RYZEN 9 3900XT 12-CORE 24 14,660 351,840 AMD
15 CORE I9-7920X CPU @ 2.90GHZ 24 14,222 341,328 Intel
16 EPYC 7401P 24-CORE 48 7,102 340,896 AMD
17 XEON CPU E5-2690 V4 @ 2.60GHZ 28 11,999 335,972 Intel
18 RYZEN 7 5700G 16 20,849 333,584 AMD
19 12TH GEN CORE I5-12600K 16 20,849 333,584 Intel
20 11TH GEN CORE I5-11600K @ 3.90GHZ 12 27,458 329,496 Intel
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 RYZEN 9 3900X 12-CORE 24 12,821 307,704 AMD
25 CORE I9-7940X CPU @ 3.10GHZ 28 10,545 295,260 Intel
26 GENUINE 0000 @ 1.80GHZ 16 17,849 285,584 Intel
27 CORE I7-10700T CPU @ 2.00GHZ 16 17,584 281,344 Intel
28 RYZEN 5 5600X 6-CORE 12 22,607 271,284 AMD
29 XEON CPU E5-2680 V2 @ 2.80GHZ 40 6,677 267,080 Intel
30 RYZEN 7 5800H 16 16,109 257,744 AMD
31 CORE I9-10900X CPU @ 3.70GHZ 20 12,499 249,980 Intel
32 RYZEN 5 PRO 5650G 12 20,726 248,712 AMD
33 XEON CPU E5-2680 V3 @ 2.50GHZ 24 10,116 242,784 Intel
34 CORE I7-6950X CPU @ 3.00GHZ 20 11,996 239,920 Intel
35 EPYC 7V12 64-CORE 64 3,659 234,176 AMD
36 RYZEN 9 5900 12-CORE 24 9,417 226,008 AMD
37 CORE I9-9900X CPU @ 3.50GHZ 20 11,234 224,680 Intel
38 CORE I9-9900K CPU @ 3.60GHZ 16 13,411 214,576 Intel
39 CORE I5-10600 CPU @ 3.30GHZ 12 17,294 207,528 Intel
40 XEON CPU E5-2665 0 @ 2.40GHZ 32 6,408 205,056 Intel
41 RYZEN 7 PRO 4750G 16 12,539 200,624 AMD
42 XEON CPU E5-2650 V2 @ 2.60GHZ 32 6,153 196,896 Intel
43 RYZEN 5 3600 6-CORE 12 16,120 193,440 AMD
44 RYZEN 7 2700X EIGHT-CORE 16 11,468 183,488 AMD
45 CORE I5-10400 CPU @ 2.90GHZ 12 14,628 175,536 Intel
46 CORE I7-10700K CPU @ 3.80GHZ 16 10,808 172,928 Intel
47 11TH GEN CORE I9-11900F @ 2.50GHZ 16 10,179 162,864 Intel
48 XEON CPU E5-2698 V4 @ 2.20GHZ 16 9,997 159,952 Intel
49 RYZEN 7 3700X 8-CORE 16 9,893 158,288 AMD
50 CORE I7-9750H CPU @ 2.60GHZ 12 13,172 158,064 Intel
51 RYZEN 7 1800X EIGHT-CORE 16 9,446 151,136 AMD
52 RYZEN 5 2600X SIX-CORE 12 11,305 135,660 AMD
53 RYZEN 5 2600 SIX-CORE 12 11,248 134,976 AMD
54 CORE I7-10700 CPU @ 2.90GHZ 16 8,189 131,024 Intel
55 XEON GOLD 6128 CPU @ 3.40GHZ 12 10,830 129,960 Intel
56 RYZEN 5 1600 SIX-CORE 12 9,298 111,576 AMD
57 11TH GEN CORE I5-11400 @ 2.60GHZ 12 8,966 107,592 Intel
58 CORE I9-8950HK CPU @ 2.90GHZ 12 8,426 101,112 Intel
59 APPLE M1 PRO 10 8,863 88,630 Apple
60 XEON CPU E5-2680 0 @ 2.70GHZ 16 5,073 81,168 Intel
61 XEON CPU E5-2620 V3 @ 2.40GHZ 12 5,116 61,392 Intel
62 XEON CPU X5650 @ 2.67GHZ 12 4,350 52,200 Intel
63 CORE I7-8850H CPU @ 2.60GHZ 12 4,159 49,908 Intel
64 XEON CPU E5-2620 0 @ 2.00GHZ 12 3,815 45,780 Intel
65 XEON CPU E5-2697 V2 @ 2.70GHZ 24 1,608 38,592 Intel