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 Tuesday, 27 September 2022 13:39:56

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 Tuesday, 27 September 2022 13:39:56

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 5900X 12-CORE 24 25,876 621,024 AMD
3 12TH GEN CORE I7-12700K 20 29,976 599,520 Intel
4 RYZEN 9 5950X 16-CORE 32 18,011 576,352 AMD
5 12TH GEN CORE I5-12600K 16 33,180 530,880 Intel
6 12TH GEN CORE I9-12900K 24 18,254 438,096 Intel
7 RYZEN 7 5700X 8-CORE 16 25,634 410,144 AMD
8 RYZEN 9 3900 12-CORE 24 16,951 406,824 AMD
9 RYZEN 7 5700G 16 25,013 400,208 AMD
10 RYZEN 9 3900X 12-CORE 24 14,328 343,872 AMD
11 RYZEN 9 3950X 16-CORE 32 10,502 336,064 AMD
12 11TH GEN CORE I9-11900K @ 3.50GHZ 16 20,707 331,312 Intel
13 RYZEN 9 3900XT 12-CORE 24 13,067 313,608 AMD
14 11TH GEN CORE I7-11700K @ 3.60GHZ 16 18,894 302,304 Intel
15 RYZEN 7 3800X 8-CORE 16 17,664 282,624 AMD
16 RYZEN 7 5800H 16 17,584 281,344 AMD
17 XEON CPU E5-2680 V3 @ 2.50GHZ 24 11,149 267,576 Intel
18 CORE I9-10850K CPU @ 3.60GHZ 20 12,475 249,500 Intel
19 CORE I9-7920X CPU @ 2.90GHZ 24 10,355 248,520 Intel
20 RYZEN 5 5600X 6-CORE 12 20,010 240,120 AMD
21 XEON CPU E5-2680 V2 @ 2.80GHZ 40 5,921 236,840 Intel
22 XEON CPU E5-2690 V4 @ 2.60GHZ 28 8,393 235,004 Intel
23 RYZEN THREADRIPPER 2950X 16-CORE 32 7,333 234,656 AMD
24 EPYC 7401P 24-CORE 48 4,616 221,568 AMD
25 CORE I9-10900X CPU @ 3.70GHZ 20 10,803 216,060 Intel
26 RYZEN 9 5900HS 16 13,288 212,608 AMD
27 CORE I9-9900K CPU @ 3.60GHZ 16 12,709 203,344 Intel
28 RYZEN 5 5600G 12 16,860 202,320 AMD
29 12TH GEN CORE I3-12100F 8 23,739 189,912 Intel
30 CORE I7-9700 CPU @ 3.00GHZ 8 22,943 183,544 Intel
31 CORE I7-8700 CPU @ 3.20GHZ 12 13,824 165,888 Intel
32 RYZEN 7 PRO 4750G 16 10,199 163,184 AMD
33 CORE I7-9700K CPU @ 3.60GHZ 8 20,224 161,792 Intel
34 APPLE M1 MAX 10 15,910 159,100 Apple
35 RYZEN 5 2600X SIX-CORE 12 13,175 158,100 AMD
36 CORE I7-10750H CPU @ 2.60GHZ 12 13,098 157,176 Intel
37 CORE I7-10700 CPU @ 2.90GHZ 16 9,270 148,320 Intel
38 XEON CPU E5-2698 V4 @ 2.20GHZ 16 9,083 145,328 Intel
39 RYZEN 5 3600 6-CORE 12 11,448 137,376 AMD
40 CORE I7-7700K CPU @ 4.20GHZ 8 16,069 128,552 Intel
41 CORE I7-4790 CPU @ 3.60GHZ 8 15,275 122,200 Intel
42 RYZEN 7 3700X 8-CORE 16 7,338 117,408 AMD
43 11TH GEN CORE I5-11400 @ 2.60GHZ 12 9,762 117,144 Intel
44 RYZEN 7 4800H 16 7,290 116,640 AMD
45 11TH GEN CORE I9-11900F @ 2.50GHZ 16 6,522 104,352 Intel
46 RYZEN 5 2600 SIX-CORE 12 8,665 103,980 AMD
47 GENUINE CPU 0000 @ 2.70GHZ 8 12,097 96,776 Intel
48 CORE I5-10400 CPU @ 2.90GHZ 12 7,941 95,292 Intel
49 CORE I7-10700T CPU @ 2.00GHZ 16 5,680 90,880 Intel
50 RYZEN 5 1600 SIX-CORE 12 6,405 76,860 AMD
51 CORE I7-8705G CPU @ 3.10GHZ 8 9,013 72,104 Intel
52 XEON CPU E3-1270 V5 @ 3.60GHZ 8 8,819 70,552 Intel
53 CORE I3-10105F CPU @ 3.70GHZ 8 8,602 68,816 Intel
54 CORE I7-4790K CPU @ 4.00GHZ 8 8,220 65,760 Intel
55 CORE I5-8600T CPU @ 2.30GHZ 6 10,908 65,448 Intel
56 EPYC 7251 8-CORE 16 4,048 64,768 AMD
57 CORE I7-6700K CPU @ 4.00GHZ 8 7,990 63,920 Intel
58 RYZEN 5 5500U 12 5,276 63,312 AMD
59 XEON CPU E5-1630 V3 @ 3.70GHZ 8 7,704 61,632 Intel
60 11TH GEN CORE I5-1135G7 @ 2.40GHZ 8 7,565 60,520 Intel
61 XEON CPU E5-2680 0 @ 2.70GHZ 16 3,635 58,160 Intel
62 CORE I7-4770HQ CPU @ 2.20GHZ 8 6,325 50,600 Intel
63 CORE I7-4790T CPU @ 2.70GHZ 8 6,265 50,120 Intel
64 CORE I7-3770 CPU @ 3.40GHZ 8 6,021 48,168 Intel
65 APPLE M1 PRO 10 4,653 46,530 Apple
66 RYZEN 5 3500X 6-CORE 6 7,602 45,612 AMD
67 CORE I7-4770 CPU @ 3.40GHZ 8 5,555 44,440 Intel
68 CORE I5-8265U CPU @ 1.60GHZ 8 4,523 36,184 Intel
69 RYZEN 5 PRO 2400G 8 4,447 35,576 AMD
70 XEON CPU E3-1245 V2 @ 3.40GHZ 8 4,445 35,560 Intel
71 XEON CPU E5-2650L V4 @ 1.70GHZ 28 1,261 35,308 Intel
72 XEON CPU E31245 @ 3.30GHZ 8 4,097 32,776 Intel
73 RYZEN 5 2400G 8 3,678 29,424 AMD
74 CORE I7-2760QM CPU @ 2.40GHZ 8 2,859 22,872 Intel
75 CORE I7 CPU 975 @ 3.33GHZ 8 2,304 18,432 Intel