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: 0xa8

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

PPDDB data as of Saturday, 28 January 2023 00:14:36

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 Saturday, 28 January 2023 00:14:36

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 RYZEN 9 7950X 16-CORE 32 20,713 662,816 AMD
2 RYZEN 7 5800X 8-CORE 16 40,856 653,696 AMD
3 RYZEN 7 5800X3D 8-CORE 16 39,678 634,848 AMD
4 12TH GEN CORE I7-12700K 20 29,976 599,520 Intel
5 RYZEN 7 7700X 8-CORE 16 36,388 582,208 AMD
6 12TH GEN CORE I5-12600K 16 31,466 503,456 Intel
7 RYZEN 9 5900X 12-CORE 24 20,246 485,904 AMD
8 RYZEN 9 5950X 16-CORE 32 14,949 478,368 AMD
9 RYZEN 7 5700G 16 27,544 440,704 AMD
10 RYZEN 7 5700X 8-CORE 16 26,064 417,024 AMD
11 RYZEN 9 3900 12-CORE 24 16,951 406,824 AMD
12 RYZEN 9 3950X 16-CORE 32 10,502 336,064 AMD
13 11TH GEN CORE I9-11900K @ 3.50GHZ 16 20,707 331,312 Intel
14 RYZEN 9 3900XT 12-CORE 24 13,067 313,608 AMD
15 RYZEN 9 3900X 12-CORE 24 13,012 312,288 AMD
16 11TH GEN CORE I7-11700K @ 3.60GHZ 16 18,894 302,304 Intel
17 RYZEN 7 5800H 16 18,740 299,840 AMD
18 RYZEN 7 3800X 8-CORE 16 16,975 271,600 AMD
19 12TH GEN CORE I9-12900K 24 11,232 269,568 Intel
20 XEON CPU E5-2680 V3 @ 2.50GHZ 24 11,149 267,576 Intel
21 CORE I9-7920X CPU @ 2.90GHZ 24 10,355 248,520 Intel
22 XEON CPU E5-2680 V2 @ 2.80GHZ 40 5,921 236,840 Intel
23 XEON CPU E5-2690 V4 @ 2.60GHZ 28 8,393 235,004 Intel
24 RYZEN THREADRIPPER 2950X 16-CORE 32 7,333 234,656 AMD
25 CORE I9-10850K CPU @ 3.60GHZ 20 11,677 233,540 Intel
26 CORE I9-7940X CPU @ 3.10GHZ 28 7,955 222,740 Intel
27 EPYC 7401P 24-CORE 48 4,616 221,568 AMD
28 RYZEN 5 5600X 6-CORE 12 18,195 218,340 AMD
29 CORE I9-10900X CPU @ 3.70GHZ 20 10,803 216,060 Intel
30 RYZEN 9 5900HS 16 13,288 212,608 AMD
31 CORE I9-9900K CPU @ 3.60GHZ 16 12,709 203,344 Intel
32 RYZEN 5 5600G 12 16,860 202,320 AMD
33 12TH GEN CORE I3-12100F 8 23,739 189,912 Intel
34 CORE I7-9700 CPU @ 3.00GHZ 8 22,943 183,544 Intel
35 CORE I7-8700 CPU @ 3.20GHZ 12 13,776 165,312 Intel
36 RYZEN 7 PRO 4750G 16 10,011 160,176 AMD
37 APPLE M1 MAX 10 15,910 159,100 Apple
38 CORE I7-10750H CPU @ 2.60GHZ 12 13,098 157,176 Intel
39 CORE I7-9700K CPU @ 3.60GHZ 8 18,919 151,352 Intel
40 CORE I7-10700 CPU @ 2.90GHZ 16 9,270 148,320 Intel
41 XEON CPU E5-2698 V4 @ 2.20GHZ 16 9,083 145,328 Intel
42 RYZEN 5 3600 6-CORE 12 12,030 144,360 AMD
43 RYZEN 5 2600X SIX-CORE 12 10,796 129,552 AMD
44 CORE I7-4790 CPU @ 3.60GHZ 8 15,275 122,200 Intel
45 RYZEN 7 3700X 8-CORE 16 7,338 117,408 AMD
46 RYZEN 7 4800H 16 7,290 116,640 AMD
47 CORE I7-7700K CPU @ 4.20GHZ 8 13,967 111,736 Intel
48 11TH GEN CORE I9-11900F @ 2.50GHZ 16 6,522 104,352 Intel
49 RYZEN 5 2600 SIX-CORE 12 8,665 103,980 AMD
50 XEON CPU E5-2650 V2 @ 2.60GHZ 32 3,056 97,792 Intel
51 GENUINE CPU 0000 @ 2.70GHZ 8 12,097 96,776 Intel
52 CORE I5-10400 CPU @ 2.90GHZ 12 7,941 95,292 Intel
53 CORE I7-10700T CPU @ 2.00GHZ 16 5,680 90,880 Intel
54 11TH GEN CORE I5-11400 @ 2.60GHZ 12 7,544 90,528 Intel
55 XEON CPU E5-2670 0 @ 2.60GHZ 32 2,612 83,584 Intel
56 CORE I7-8705G CPU @ 3.10GHZ 8 10,124 80,992 Intel
57 CORE I9-8950HK CPU @ 2.90GHZ 12 6,458 77,496 Intel
58 RYZEN 5 1600 SIX-CORE 12 6,405 76,860 AMD
59 RYZEN 7 2700X EIGHT-CORE 16 4,739 75,824 AMD
60 XEON CPU E3-1270 V5 @ 3.60GHZ 8 8,819 70,552 Intel
61 CORE I3-10105F CPU @ 3.70GHZ 8 8,602 68,816 Intel
62 CORE I7-4790K CPU @ 4.00GHZ 8 8,220 65,760 Intel
63 CORE I7-6700K CPU @ 4.00GHZ 8 8,215 65,720 Intel
64 CORE I5-8600T CPU @ 2.30GHZ 6 10,908 65,448 Intel
65 EPYC 7251 8-CORE 16 4,048 64,768 AMD
66 APPLE M1 8 8,065 64,520 Apple
67 RYZEN 5 5500U 12 5,276 63,312 AMD
68 CORE I5-9500 CPU @ 3.00GHZ 6 10,551 63,306 Intel
69 XEON CPU E5-1630 V3 @ 3.70GHZ 8 7,704 61,632 Intel
70 11TH GEN CORE I5-1135G7 @ 2.40GHZ 8 7,565 60,520 Intel
71 XEON CPU E5-2680 0 @ 2.70GHZ 16 3,675 58,800 Intel
72 CORE I7-4770HQ CPU @ 2.20GHZ 8 6,325 50,600 Intel
73 CORE I7-4790T CPU @ 2.70GHZ 8 6,265 50,120 Intel
74 11TH GEN CORE I7-1165G7 @ 2.80GHZ 8 6,137 49,096 Intel
75 CORE I7-3770 CPU @ 3.40GHZ 8 6,021 48,168 Intel
76 APPLE M1 PRO 10 4,653 46,530 Apple
77 RYZEN 5 3500X 6-CORE 6 7,602 45,612 AMD
78 CORE I7-4770 CPU @ 3.40GHZ 8 5,555 44,440 Intel
79 CORE I5-8265U CPU @ 1.60GHZ 8 4,523 36,184 Intel
80 RYZEN 5 PRO 2400G 8 4,447 35,576 AMD
81 XEON CPU E3-1245 V2 @ 3.40GHZ 8 4,445 35,560 Intel
82 XEON CPU E5-2650L V4 @ 1.70GHZ 28 1,261 35,308 Intel
83 CORE I7-4770K CPU @ 3.50GHZ 8 4,311 34,488 Intel
84 XEON CPU E31245 @ 3.30GHZ 8 4,097 32,776 Intel
85 RYZEN 5 2400G 8 3,678 29,424 AMD
86 CORE I5-10210U CPU @ 1.60GHZ 7 4,170 29,190 Intel
87 XEON CPU E5-2697 V2 @ 2.70GHZ 24 1,158 27,792 Intel
88 CORE I7-2760QM CPU @ 2.40GHZ 8 2,859 22,872 Intel
89 CORE I7 CPU 975 @ 3.33GHZ 8 2,304 18,432 Intel
90 CORE I7-4700MQ CPU @ 2.40GHZ 8 1,302 10,416 Intel