PROJECT #18404 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: 24,700

Core: 0xa8

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

PPDDB data as of Sunday, 04 December 2022 18:13:20

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 Sunday, 04 December 2022 18:13:20

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 RYZEN 9 3950X 16-CORE 32 32,903 1,052,896 AMD
2 RYZEN 9 7950X 16-CORE 32 25,964 830,848 AMD
3 RYZEN 7 5800X 8-CORE 16 43,448 695,168 AMD
4 RYZEN 7 7700X 8-CORE 16 41,735 667,760 AMD
5 RYZEN 7 5700G 16 41,431 662,896 AMD
6 RYZEN 7 5800X3D 8-CORE 16 38,637 618,192 AMD
7 12TH GEN CORE I9-12900K 24 24,851 596,424 Intel
8 RYZEN 9 5950X 16-CORE 32 17,376 556,032 AMD
9 RYZEN 9 3900 12-CORE 24 19,867 476,808 AMD
10 RYZEN 9 5900X 12-CORE 24 19,850 476,400 AMD
11 RYZEN 7 5700X 8-CORE 16 29,600 473,600 AMD
12 12TH GEN CORE I7-12700K 20 21,897 437,940 Intel
13 11TH GEN CORE I9-11900K @ 3.50GHZ 16 26,791 428,656 Intel
14 12TH GEN CORE I5-12600K 16 26,535 424,560 Intel
15 RYZEN THREADRIPPER 3960X 24-CORE 48 7,346 352,608 AMD
16 RYZEN 7 3800X 8-CORE 16 20,306 324,896 AMD
17 12TH GEN CORE I5-12400 12 24,136 289,632 Intel
18 CORE I9-10900X CPU @ 3.70GHZ 20 14,317 286,340 Intel
19 RYZEN 9 3900X 12-CORE 24 11,882 285,168 AMD
20 RYZEN 9 5900 12-CORE 24 11,212 269,088 AMD
21 RYZEN 5 3600X 6-CORE 12 20,499 245,988 AMD
22 RYZEN 9 5900HS 16 14,873 237,968 AMD
23 CORE I7-8700 CPU @ 3.20GHZ 12 19,428 233,136 Intel
24 RYZEN 5 5600G 12 18,250 219,000 AMD
25 CORE I7-9700K CPU @ 3.60GHZ 8 27,062 216,496 Intel
26 RYZEN 5 5600X 6-CORE 12 17,496 209,952 AMD
27 XEON CPU E5-2690 V4 @ 2.60GHZ 28 7,192 201,376 Intel
28 CORE I7-5960X CPU @ 3.00GHZ 16 12,310 196,960 Intel
29 11TH GEN CORE I7-11700K @ 3.60GHZ 16 12,238 195,808 Intel
30 RYZEN 7 2700X EIGHT-CORE 16 12,218 195,488 AMD
31 XEON CPU E5-2680 V3 @ 2.50GHZ 24 8,048 193,152 Intel
32 XEON CPU E5-2698 V4 @ 2.20GHZ 16 12,041 192,656 Intel
33 APPLE M1 MAX 10 19,238 192,380 Apple
34 RYZEN 7 5800H 16 11,691 187,056 AMD
35 RYZEN 5 3600 6-CORE 12 15,390 184,680 AMD
36 RYZEN 7 PRO 4750G 16 11,424 182,784 AMD
37 CORE I9-9900 CPU @ 3.10GHZ 16 11,163 178,608 Intel
38 CORE I7-10700T CPU @ 2.00GHZ 16 10,638 170,208 Intel
39 12TH GEN CORE I9-12900H 20 7,819 156,380 Intel
40 CORE I7-9700 CPU @ 3.00GHZ 8 18,677 149,416 Intel
41 EPYC 7401P 24-CORE 48 2,931 140,688 AMD
42 RYZEN 9 3900XT 12-CORE 24 5,841 140,184 AMD
43 CORE I7-7700K CPU @ 4.20GHZ 8 16,533 132,264 Intel
44 XEON CPU E5-2650 V2 @ 2.60GHZ 32 3,515 112,480 Intel
45 11TH GEN CORE I5-11400 @ 2.60GHZ 12 9,373 112,476 Intel
46 RYZEN 5 2600X SIX-CORE 12 9,351 112,212 AMD
47 RYZEN 5 1600 SIX-CORE 12 7,817 93,804 AMD
48 CORE I7-4790K CPU @ 4.00GHZ 8 11,700 93,600 Intel
49 CORE I5-10400 CPU @ 2.90GHZ 12 7,466 89,592 Intel
50 CORE I7-8705G CPU @ 3.10GHZ 8 10,588 84,704 Intel
51 CORE I9-8950HK CPU @ 2.90GHZ 12 6,979 83,748 Intel
52 RYZEN 7 3700X 8-CORE 16 5,151 82,416 AMD
53 CORE I5-9400F CPU @ 2.90GHZ 6 13,345 80,070 Intel
54 CORE I7-4770K CPU @ 3.50GHZ 8 9,561 76,488 Intel
55 CORE I5-9500 CPU @ 3.00GHZ 6 12,580 75,480 Intel
56 APPLE M1 8 9,236 73,888 Apple
57 XEON CPU E5-2680 0 @ 2.70GHZ 16 4,566 73,056 Intel
58 CORE I3-10100 CPU @ 3.60GHZ 8 8,678 69,424 Intel
59 11TH GEN CORE I5-1135G7 @ 2.40GHZ 8 8,657 69,256 Intel
60 CORE I7-10750H CPU @ 2.60GHZ 12 5,568 66,816 Intel
61 CORE I7-4770HQ CPU @ 2.20GHZ 8 7,678 61,424 Intel
62 CORE I7-3770 CPU @ 3.40GHZ 8 7,314 58,512 Intel
63 CORE I7-6700 CPU @ 3.40GHZ 8 6,973 55,784 Intel
64 CORE I7-5820K CPU @ 3.30GHZ 12 4,518 54,216 Intel
65 CORE I7-4790T CPU @ 2.70GHZ 8 6,521 52,168 Intel
66 CORE I7-6700K CPU @ 4.00GHZ 8 5,893 47,144 Intel
67 XEON CPU E5-2697 V2 @ 2.70GHZ 24 1,796 43,104 Intel
68 CORE I5-8265U CPU @ 1.60GHZ 8 4,870 38,960 Intel
69 XEON CPU E3-1240 V2 @ 3.40GHZ 8 4,720 37,760 Intel
70 CORE I5-10210U CPU @ 1.60GHZ 7 5,307 37,149 Intel
71 XEON CPU E31245 @ 3.30GHZ 8 3,658 29,264 Intel
72 XEON CPU E5-2620 0 @ 2.00GHZ 12 2,366 28,392 Intel
73 RYZEN 7 3700U 8 2,892 23,136 AMD