PROJECT #18422 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: 80,500

Core: 0xa8

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

PPDDB data as of Friday, 03 February 2023 06:15:10

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 Friday, 03 February 2023 06:15:10

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 13TH GEN CORE I9-13900KS 32 34,386 1,100,352 Intel
2 RYZEN 9 5950X 16-CORE 32 23,343 746,976 AMD
3 RYZEN 7 7700X 8-CORE 16 39,275 628,400 AMD
4 12TH GEN CORE I7-12700K 20 30,831 616,620 Intel
5 12TH GEN CORE I9-12900K 24 23,920 574,080 Intel
6 RYZEN 7 5700G 16 35,700 571,200 AMD
7 RYZEN 7 5800X3D 8-CORE 16 31,607 505,712 AMD
8 RYZEN 7 5700X 8-CORE 16 29,997 479,952 AMD
9 RYZEN 7 5800X 8-CORE 16 29,628 474,048 AMD
10 RYZEN 9 3950X 16-CORE 32 13,682 437,824 AMD
11 RYZEN 9 3900 12-CORE 24 17,924 430,176 AMD
12 RYZEN 9 5900X 12-CORE 24 17,654 423,696 AMD
13 CORE I9-7920X CPU @ 2.90GHZ 24 17,442 418,608 Intel
14 11TH GEN CORE I7-11700K @ 3.60GHZ 16 25,332 405,312 Intel
15 12TH GEN CORE I7-12700 20 20,245 404,900 Intel
16 RYZEN 9 3900XT 12-CORE 24 15,344 368,256 AMD
17 RYZEN 9 3900X 12-CORE 24 15,230 365,520 AMD
18 CORE I9-7940X CPU @ 3.10GHZ 28 12,129 339,612 Intel
19 12TH GEN CORE I5-12400 12 27,333 327,996 Intel
20 RYZEN 7 3800X 8-CORE 16 19,689 315,024 AMD
21 XEON CPU E5-2690 V4 @ 2.60GHZ 28 11,248 314,944 Intel
22 RYZEN 5 5600X 6-CORE 12 23,961 287,532 AMD
23 XEON CPU E5-2680 V2 @ 2.80GHZ 40 7,032 281,280 Intel
24 XEON CPU E5-2680 V3 @ 2.50GHZ 24 10,279 246,696 Intel
25 CORE I7-8700 CPU @ 3.20GHZ 12 18,955 227,460 Intel
26 CORE I9-10900X CPU @ 3.70GHZ 20 11,326 226,520 Intel
27 CORE I9-9900K CPU @ 3.60GHZ 16 14,108 225,728 Intel
28 CORE I9-9900 CPU @ 3.10GHZ 16 13,906 222,496 Intel
29 CORE I7-10700 CPU @ 2.90GHZ 16 13,556 216,896 Intel
30 RYZEN 5 5600G 12 17,668 212,016 AMD
31 RYZEN 5 3600 6-CORE 12 17,379 208,548 AMD
32 XEON CPU E5-2665 0 @ 2.40GHZ 32 6,377 204,064 Intel
33 CORE I7-10700K CPU @ 3.80GHZ 16 12,690 203,040 Intel
34 XEON CPU E5-2698 V4 @ 2.20GHZ 16 12,116 193,856 Intel
35 RYZEN 7 PRO 4750G 16 11,687 186,992 AMD
36 RYZEN 7 3700X 8-CORE 16 11,093 177,488 AMD
37 11TH GEN CORE I9-11900F @ 2.50GHZ 16 10,194 163,104 Intel
38 CORE I7-5930K CPU @ 3.50GHZ 12 13,386 160,632 Intel
39 EPYC 7401P 24-CORE 48 3,188 153,024 AMD
40 CORE I5-10400 CPU @ 2.90GHZ 12 12,161 145,932 Intel
41 XEON CPU E5-2650 V2 @ 2.60GHZ 32 4,380 140,160 Intel
42 XEON CPU E5-2650L V4 @ 1.70GHZ 28 4,976 139,328 Intel
43 11TH GEN CORE I5-11400 @ 2.60GHZ 12 11,392 136,704 Intel
44 RYZEN 7 2700X EIGHT-CORE 16 7,872 125,952 AMD
45 CORE I7-10700T CPU @ 2.00GHZ 16 7,606 121,696 Intel
46 CORE I7-9750H CPU @ 2.60GHZ 12 10,076 120,912 Intel
47 CORE I9-8950HK CPU @ 2.90GHZ 12 9,986 119,832 Intel
48 CORE I7-5820K CPU @ 3.30GHZ 12 9,719 116,628 Intel
49 RYZEN 5 1600 SIX-CORE 12 9,105 109,260 AMD
50 APPLE M1 PRO 10 7,772 77,720 Apple
51 XEON CPU E5-2680 0 @ 2.70GHZ 16 4,595 73,520 Intel
52 XEON CPU E5-2697 V2 @ 2.70GHZ 24 2,236 53,664 Intel