PROJECT #18420 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
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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 11TH GEN CORE I5-11400 @ 2.60GHZ 12 235,038 2,820,456 Intel
2 13TH GEN CORE I9-13900KS 32 34,120 1,091,840 Intel
3 RYZEN 9 7950X 16-CORE 32 27,620 883,840 AMD
4 RYZEN 9 5950X 16-CORE 32 19,107 611,424 AMD
5 12TH GEN CORE I9-12900K 24 23,180 556,320 Intel
6 RYZEN 7 5800X3D 8-CORE 16 32,661 522,576 AMD
7 RYZEN 7 5700X 8-CORE 16 32,618 521,888 AMD
8 12TH GEN CORE I7-12700K 20 25,834 516,680 Intel
9 RYZEN 9 3950X 16-CORE 32 15,761 504,352 AMD
10 RYZEN 7 5800X 8-CORE 16 29,792 476,672 AMD
11 12TH GEN CORE I7-12700 20 21,351 427,020 Intel
12 RYZEN 7 7700X 8-CORE 16 26,010 416,160 AMD
13 11TH GEN CORE I7-11700K @ 3.60GHZ 16 24,792 396,672 Intel
14 CORE I7-5930K CPU @ 3.50GHZ 12 30,553 366,636 Intel
15 RYZEN 9 3900XT 12-CORE 24 15,249 365,976 AMD
16 RYZEN 5 3600X 6-CORE 12 29,444 353,328 AMD
17 RYZEN 7 5700G 16 20,979 335,664 AMD
18 RYZEN 9 5900X 12-CORE 24 13,694 328,656 AMD
19 XEON CPU E5-2690 V4 @ 2.60GHZ 28 11,699 327,572 Intel
20 RYZEN 9 3900X 12-CORE 24 11,860 284,640 AMD
21 CORE I9-9900K CPU @ 3.60GHZ 16 17,305 276,880 Intel
22 RYZEN 7 3700X 8-CORE 16 16,849 269,584 AMD
23 RYZEN 5 PRO 5650G 12 22,406 268,872 AMD
24 RYZEN THREADRIPPER 2950X 16-CORE 32 7,751 248,032 AMD
25 RYZEN 5 5600X 6-CORE 12 20,282 243,384 AMD
26 RYZEN 7 2700 EIGHT-CORE 16 15,133 242,128 AMD
27 XEON CPU E5-2680 V3 @ 2.50GHZ 24 9,486 227,664 Intel
28 RYZEN 7 3800X 8-CORE 16 13,849 221,584 AMD
29 CORE I7-8700 CPU @ 3.20GHZ 12 18,066 216,792 Intel
30 RYZEN 7 PRO 4750G 16 12,433 198,928 AMD
31 RYZEN 5 5600G 12 16,533 198,396 AMD
32 CORE I7-6800K CPU @ 3.40GHZ 12 15,043 180,516 Intel
33 12TH GEN CORE I9-12900H 20 8,845 176,900 Intel
34 RYZEN 5 3600 6-CORE 12 14,489 173,868 AMD
35 XEON CPU E5-2698 V4 @ 2.20GHZ 16 10,825 173,200 Intel
36 XEON CPU E5-2650 V2 @ 2.60GHZ 32 5,263 168,416 Intel
37 XEON CPU E5-2670 0 @ 2.60GHZ 32 5,086 162,752 Intel
38 CORE I9-9900KF CPU @ 3.60GHZ 16 9,493 151,888 Intel
39 RYZEN 5 2600 SIX-CORE 12 12,220 146,640 AMD
40 CORE I7-9750H CPU @ 2.60GHZ 12 10,917 131,004 Intel
41 CORE I7-10700 CPU @ 2.90GHZ 16 7,735 123,760 Intel
42 XEON CPU E5-2650L V4 @ 1.70GHZ 28 4,305 120,540 Intel
43 12TH GEN CORE I5-12600K 16 7,100 113,600 Intel
44 CORE I7-10700T CPU @ 2.00GHZ 16 7,085 113,360 Intel
45 RYZEN 7 1700 EIGHT-CORE 16 6,866 109,856 AMD
46 11TH GEN CORE I5-11400F @ 2.60GHZ 12 8,628 103,536 Intel
47 RYZEN 5 1600 SIX-CORE 12 8,499 101,988 AMD
48 RYZEN 7 2700X EIGHT-CORE 16 6,342 101,472 AMD
49 CORE I9-8950HK CPU @ 2.90GHZ 12 8,390 100,680 Intel
50 XEON GOLD 6128 CPU @ 3.40GHZ 12 7,475 89,700 Intel
51 CORE I5-10400 CPU @ 2.90GHZ 12 6,901 82,812 Intel
52 XEON CPU E5-2697 V2 @ 2.70GHZ 24 3,095 74,280 Intel
53 XEON CPU E5-2680 0 @ 2.70GHZ 16 4,475 71,600 Intel
54 XEON CPU E5-2620 0 @ 2.00GHZ 12 2,692 32,304 Intel