PROJECT #18419 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 Thursday, 30 June 2022 00:49:54

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 Thursday, 30 June 2022 00:49:54

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 42,836 685,376 AMD
2 RYZEN 9 5950X 16-CORE 32 21,043 673,376 AMD
3 RYZEN 9 5900X 12-CORE 24 27,828 667,872 AMD
4 RYZEN 9 3950X 16-CORE 32 20,605 659,360 AMD
5 RYZEN 7 2700X EIGHT-CORE 16 28,652 458,432 AMD
6 12TH GEN CORE I9-12900K 24 19,024 456,576 Intel
7 RYZEN 7 5700X 8-CORE 16 28,524 456,384 AMD
8 11TH GEN CORE I9-11900K @ 3.50GHZ 16 21,501 344,016 Intel
9 11TH GEN CORE I7-11700K @ 3.60GHZ 16 21,395 342,320 Intel
10 RYZEN 9 3900XT 12-CORE 24 13,138 315,312 AMD
11 RYZEN 9 3900X 12-CORE 24 12,133 291,192 AMD
12 RYZEN 7 3800X 8-CORE 16 17,860 285,760 AMD
13 CORE I9-10900X CPU @ 3.70GHZ 20 12,847 256,940 Intel
14 RYZEN 9 5900HS 16 13,603 217,648 AMD
15 CORE I7-8700 CPU @ 3.20GHZ 12 18,068 216,816 Intel
16 CORE I7-5960X CPU @ 3.00GHZ 16 13,272 212,352 Intel
17 RYZEN 7 5800H 16 12,767 204,272 AMD
18 RYZEN 5 5600X 6-CORE 12 16,980 203,760 AMD
19 RYZEN 5 3600X 6-CORE 12 16,277 195,324 AMD
20 RYZEN 7 PRO 4750G 16 11,642 186,272 AMD
21 XEON CPU E5-2680 V3 @ 2.50GHZ 24 7,521 180,504 Intel
22 11TH GEN CORE I9-11900F @ 2.50GHZ 16 10,704 171,264 Intel
23 11TH GEN CORE I7-1185G7 @ 3.00GHZ 8 20,661 165,288 Intel
24 RYZEN 5 3600 6-CORE 12 13,508 162,096 AMD
25 XEON CPU E5-2698 V4 @ 2.20GHZ 16 9,905 158,480 Intel
26 RYZEN 7 1700 EIGHT-CORE 16 9,831 157,296 AMD
27 CORE I5-10400 CPU @ 2.90GHZ 12 12,813 153,756 Intel
28 RYZEN 7 3700X 8-CORE 16 8,982 143,712 AMD
29 RYZEN 7 5700G 16 8,845 141,520 AMD
30 CORE I7-10700 CPU @ 2.90GHZ 16 8,024 128,384 Intel
31 CORE I7-9700K CPU @ 3.60GHZ 8 13,806 110,448 Intel
32 GENUINE CPU 0000 @ 2.70GHZ 8 13,489 107,912 Intel
33 CORE I5-8400 CPU @ 2.80GHZ 6 17,108 102,648 Intel
34 11TH GEN CORE I5-11400 @ 2.60GHZ 12 8,453 101,436 Intel
35 11TH GEN CORE I7-11850H @ 2.50GHZ 16 6,234 99,744 Intel
36 CORE I7-6700K CPU @ 4.00GHZ 8 11,629 93,032 Intel
37 CORE I3-10105F CPU @ 3.70GHZ 8 11,490 91,920 Intel
38 CORE I9-8950HK CPU @ 2.90GHZ 12 7,258 87,096 Intel
39 RYZEN 5 1600 SIX-CORE 12 6,929 83,148 AMD
40 CORE I7-4790K CPU @ 4.00GHZ 8 10,049 80,392 Intel
41 CORE I5-8350U CPU @ 1.70GHZ 8 9,703 77,624 Intel
42 CORE I7-8705G CPU @ 3.10GHZ 8 9,278 74,224 Intel
43 CORE I7-4770K CPU @ 3.50GHZ 8 8,558 68,464 Intel
44 XEON CPU E5-1630 V3 @ 3.70GHZ 8 7,950 63,600 Intel
45 CORE I5-8600T CPU @ 2.30GHZ 6 10,566 63,396 Intel
46 11TH GEN CORE I5-1135G7 @ 2.40GHZ 8 7,911 63,288 Intel
47 XEON CPU E5-2680 0 @ 2.70GHZ 16 3,916 62,656 Intel
48 CORE I7-6700HQ CPU @ 2.60GHZ 8 7,705 61,640 Intel
49 RYZEN 7 4700U 8 6,954 55,632 AMD
50 CORE I7-4770HQ CPU @ 2.20GHZ 8 6,037 48,296 Intel
51 CORE I7-3770 CPU @ 3.40GHZ 8 5,708 45,664 Intel
52 CORE I7-10610U CPU @ 1.80GHZ 8 5,604 44,832 Intel
53 XEON CPU E3-1245 V2 @ 3.40GHZ 8 5,379 43,032 Intel
54 APPLE M1 8 5,126 41,008 Apple
55 CORE I7-4765T CPU @ 2.00GHZ 8 4,732 37,856 Intel
56 XEON CPU E3-1240 V2 @ 3.40GHZ 8 4,613 36,904 Intel
57 CORE I5-10210U CPU @ 1.60GHZ 7 5,184 36,288 Intel
58 FX-8350 EIGHT-CORE 8 3,993 31,944 AMD
59 XEON CPU E31245 @ 3.30GHZ 8 3,559 28,472 Intel
60 CORE I5-7200U CPU @ 2.50GHZ 4 5,960 23,840 Intel
61 FX-6100 SIX-CORE 6 1,643 9,858 AMD