PROJECT #18416 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: 35,650

Core: GRO_A8

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

PPDDB data as of Friday, 27 May 2022 05:13:25

Rank
Project
Model Name
Folding@Home Identifier
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Brand
GPU
Model
PPD
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PROJECT FOLDING PPD AVERAGES BY CPU BETA

PPDDB data as of Friday, 27 May 2022 05:13:25

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 RYZEN 7 5800X 8-CORE 16 40,904 654,464 AMD
2 RYZEN 9 5950X 16-CORE 32 17,631 564,192 AMD
3 12TH GEN CORE I7-12700K 20 27,971 559,420 Intel
4 RYZEN 9 5900X 12-CORE 24 18,341 440,184 AMD
5 RYZEN 7 5700G 16 25,013 400,208 AMD
6 11TH GEN CORE I7-11700K @ 3.60GHZ 16 21,581 345,296 Intel
7 RYZEN 9 3900X 12-CORE 24 14,328 343,872 AMD
8 RYZEN 9 3900 12-CORE 24 14,148 339,552 AMD
9 RYZEN 9 3950X 16-CORE 32 10,502 336,064 AMD
10 11TH GEN CORE I9-11900K @ 3.50GHZ 16 20,707 331,312 Intel
11 RYZEN 9 3900XT 12-CORE 24 13,067 313,608 AMD
12 RYZEN 7 3800X 8-CORE 16 17,771 284,336 AMD
13 XEON CPU E5-2680 V3 @ 2.50GHZ 24 11,149 267,576 Intel
14 CORE I9-10850K CPU @ 3.60GHZ 20 12,475 249,500 Intel
15 CORE I9-7920X CPU @ 2.90GHZ 24 10,355 248,520 Intel
16 RYZEN 5 5600X 6-CORE 12 20,010 240,120 AMD
17 XEON CPU E5-2690 V4 @ 2.60GHZ 28 8,393 235,004 Intel
18 RYZEN THREADRIPPER 2950X 16-CORE 32 7,333 234,656 AMD
19 EPYC 7401P 24-CORE 48 4,616 221,568 AMD
20 RYZEN 9 5900HS 16 13,288 212,608 AMD
21 CORE I9-9900K CPU @ 3.60GHZ 16 12,709 203,344 Intel
22 CORE I7-9700 CPU @ 3.00GHZ 8 22,943 183,544 Intel
23 CORE I7-8700 CPU @ 3.20GHZ 12 13,824 165,888 Intel
24 CORE I7-9700K CPU @ 3.60GHZ 8 20,224 161,792 Intel
25 RYZEN 5 2600X SIX-CORE 12 13,175 158,100 AMD
26 CORE I7-10750H CPU @ 2.60GHZ 12 13,098 157,176 Intel
27 CORE I7-10700 CPU @ 2.90GHZ 16 9,270 148,320 Intel
28 CORE I9-10900X CPU @ 3.70GHZ 20 7,161 143,220 Intel
29 RYZEN 7 PRO 4750G 16 8,801 140,816 AMD
30 RYZEN 5 3600 6-CORE 12 10,847 130,164 AMD
31 CORE I7-7700K CPU @ 4.20GHZ 8 16,069 128,552 Intel
32 RYZEN 7 3700X 8-CORE 16 7,730 123,680 AMD
33 CORE I7-4790 CPU @ 3.60GHZ 8 15,275 122,200 Intel
34 11TH GEN CORE I5-11400 @ 2.60GHZ 12 9,762 117,144 Intel
35 RYZEN 7 4800H 16 7,290 116,640 AMD
36 11TH GEN CORE I9-11900F @ 2.50GHZ 16 6,522 104,352 Intel
37 RYZEN 5 2600 SIX-CORE 12 8,665 103,980 AMD
38 GENUINE CPU 0000 @ 2.70GHZ 8 12,097 96,776 Intel
39 CORE I5-10400 CPU @ 2.90GHZ 12 7,941 95,292 Intel
40 RYZEN 5 1600 SIX-CORE 12 6,437 77,244 AMD
41 CORE I7-8705G CPU @ 3.10GHZ 8 9,013 72,104 Intel
42 CORE I3-10105F CPU @ 3.70GHZ 8 8,602 68,816 Intel
43 CORE I7-4790K CPU @ 4.00GHZ 8 8,220 65,760 Intel
44 XEON CPU E5-1630 V3 @ 3.70GHZ 8 8,100 64,800 Intel
45 EPYC 7251 8-CORE 16 4,048 64,768 AMD
46 CORE I7-6700K CPU @ 4.00GHZ 8 7,990 63,920 Intel
47 XEON CPU E5-2680 0 @ 2.70GHZ 16 3,854 61,664 Intel
48 11TH GEN CORE I5-1135G7 @ 2.40GHZ 8 7,565 60,520 Intel
49 CORE I7-4790T CPU @ 2.70GHZ 8 6,265 50,120 Intel
50 CORE I7-4770HQ CPU @ 2.20GHZ 8 6,203 49,624 Intel
51 CORE I7-3770 CPU @ 3.40GHZ 8 6,021 48,168 Intel
52 RYZEN 5 3500X 6-CORE 6 7,602 45,612 AMD
53 CORE I7-4770 CPU @ 3.40GHZ 8 5,555 44,440 Intel
54 CORE I5-8265U CPU @ 1.60GHZ 8 4,523 36,184 Intel
55 RYZEN 5 PRO 2400G 8 4,447 35,576 AMD
56 XEON CPU E3-1245 V2 @ 3.40GHZ 8 4,445 35,560 Intel
57 XEON CPU E31245 @ 3.30GHZ 8 4,097 32,776 Intel
58 RYZEN 5 2400G 8 3,678 29,424 AMD
59 CORE I7 CPU 975 @ 3.33GHZ 8 2,304 18,432 Intel