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: GRO_A8

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

PPDDB data as of Monday, 03 October 2022 12:16:28

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Model Name
Folding@Home Identifier
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Model
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PROJECT FOLDING PPD AVERAGES BY CPU BETA

PPDDB data as of Monday, 03 October 2022 12:16:28

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 RYZEN 7 5800X3D 8-CORE 16 37,502 600,032 AMD
3 RYZEN 9 5950X 16-CORE 32 17,691 566,112 AMD
4 12TH GEN CORE I9-12900K 24 23,180 556,320 Intel
5 RYZEN 7 5700X 8-CORE 16 33,754 540,064 AMD
6 12TH GEN CORE I7-12700K 20 25,834 516,680 Intel
7 RYZEN 7 5800X 8-CORE 16 30,350 485,600 AMD
8 RYZEN 9 3950X 16-CORE 32 14,513 464,416 AMD
9 12TH GEN CORE I7-12700 20 21,351 427,020 Intel
10 11TH GEN CORE I7-11700K @ 3.60GHZ 16 24,792 396,672 Intel
11 RYZEN 9 5900X 12-CORE 24 16,046 385,104 AMD
12 RYZEN 9 3900XT 12-CORE 24 15,249 365,976 AMD
13 RYZEN 9 3900X 12-CORE 24 14,507 348,168 AMD
14 RYZEN 7 5700G 16 20,970 335,520 AMD
15 XEON CPU E5-2690 V4 @ 2.60GHZ 28 11,699 327,572 Intel
16 RYZEN 7 3700X 8-CORE 16 17,263 276,208 AMD
17 CORE I9-9900K CPU @ 3.60GHZ 16 16,652 266,432 Intel
18 XEON CPU E5-2650 V2 @ 2.60GHZ 32 7,625 244,000 Intel
19 RYZEN 7 2700 EIGHT-CORE 16 15,133 242,128 AMD
20 RYZEN 5 5600X 6-CORE 12 19,497 233,964 AMD
21 RYZEN THREADRIPPER 2950X 16-CORE 32 7,196 230,272 AMD
22 XEON CPU E5-2680 V3 @ 2.50GHZ 24 9,486 227,664 Intel
23 RYZEN 7 3800X 8-CORE 16 13,849 221,584 AMD
24 CORE I9-8950HK CPU @ 2.90GHZ 12 18,405 220,860 Intel
25 CORE I7-8700 CPU @ 3.20GHZ 12 18,077 216,924 Intel
26 RYZEN 7 PRO 4750G 16 12,492 199,872 AMD
27 RYZEN 5 3600 6-CORE 12 16,574 198,888 AMD
28 RYZEN 5 5600G 12 16,519 198,228 AMD
29 CORE I7-6800K CPU @ 3.40GHZ 12 15,043 180,516 Intel
30 RYZEN 5 3600X 6-CORE 12 14,619 175,428 AMD
31 XEON CPU E5-2698 V4 @ 2.20GHZ 16 10,825 173,200 Intel
32 CORE I9-9900KF CPU @ 3.60GHZ 16 9,493 151,888 Intel
33 RYZEN 5 2600 SIX-CORE 12 12,220 146,640 AMD
34 CORE I7-10700 CPU @ 2.90GHZ 16 7,735 123,760 Intel
35 CORE I7-10700T CPU @ 2.00GHZ 16 7,655 122,480 Intel
36 CORE I7-9750H CPU @ 2.60GHZ 12 10,058 120,696 Intel
37 XEON CPU E5-2650L V4 @ 1.70GHZ 28 4,305 120,540 Intel
38 12TH GEN CORE I5-12600K 16 7,100 113,600 Intel
39 RYZEN 7 1700 EIGHT-CORE 16 6,866 109,856 AMD
40 RYZEN 5 1600 SIX-CORE 12 8,499 101,988 AMD
41 XEON CPU E5-2680 0 @ 2.70GHZ 16 5,833 93,328 Intel
42 XEON GOLD 6128 CPU @ 3.40GHZ 12 7,475 89,700 Intel
43 RYZEN 7 2700X EIGHT-CORE 16 5,355 85,680 AMD
44 CORE I5-10400 CPU @ 2.90GHZ 12 6,901 82,812 Intel
45 XEON CPU E5-2620 0 @ 2.00GHZ 12 2,692 32,304 Intel