PROJECT #18406 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: 24,700

Core: GRO_A8

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

PPDDB data as of Thursday, 30 June 2022 00:49:54

Rank
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Model Name
Folding@Home Identifier
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GPU
Model
PPD
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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 9 3950X 16-CORE 32 28,018 896,576 AMD
2 RYZEN 7 5800X 8-CORE 16 46,506 744,096 AMD
3 12TH GEN CORE I7-12700K 20 32,729 654,580 Intel
4 RYZEN 9 5950X 16-CORE 32 16,802 537,664 AMD
5 RYZEN 7 5700X 8-CORE 16 31,794 508,704 AMD
6 11TH GEN CORE I9-11900K @ 3.50GHZ 16 26,272 420,352 Intel
7 11TH GEN CORE I7-11700K @ 3.60GHZ 16 25,826 413,216 Intel
8 RYZEN 7 5700G 16 23,096 369,536 AMD
9 RYZEN 9 5900X 12-CORE 24 15,358 368,592 AMD
10 RYZEN 9 3900XT 12-CORE 24 14,713 353,112 AMD
11 CORE I9-10850K CPU @ 3.60GHZ 20 17,413 348,260 Intel
12 RYZEN 7 3800X 8-CORE 16 20,400 326,400 AMD
13 RYZEN 7 5800H 16 16,100 257,600 AMD
14 RYZEN 5 5600X 6-CORE 12 21,224 254,688 AMD
15 CORE I7-8700 CPU @ 3.20GHZ 12 20,085 241,020 Intel
16 RYZEN 9 5900HS 16 14,057 224,912 AMD
17 RYZEN 5 2600X SIX-CORE 12 18,315 219,780 AMD
18 RYZEN 5 3600 6-CORE 12 16,611 199,332 AMD
19 CORE I9-9900 CPU @ 3.10GHZ 16 12,117 193,872 Intel
20 RYZEN 5 5600G 12 15,963 191,556 AMD
21 XEON CPU E5-2690 V4 @ 2.60GHZ 28 6,817 190,876 Intel
22 XEON CPU E5-2680 V3 @ 2.50GHZ 24 7,904 189,696 Intel
23 RYZEN 7 PRO 4750G 16 11,788 188,608 AMD
24 RYZEN 7 1700 EIGHT-CORE 16 11,717 187,472 AMD
25 RYZEN THREADRIPPER 3960X 24-CORE 48 3,623 173,904 AMD
26 CORE I7-9700K CPU @ 3.60GHZ 8 19,981 159,848 Intel
27 XEON CPU E5-2698 V4 @ 2.20GHZ 16 9,494 151,904 Intel
28 RYZEN 7 3700X 8-CORE 16 8,995 143,920 AMD
29 CORE I7-5820K CPU @ 3.30GHZ 12 10,030 120,360 Intel
30 CORE I7-10700T CPU @ 2.00GHZ 16 7,079 113,264 Intel
31 RYZEN 5 1600 SIX-CORE 12 7,402 88,824 AMD
32 CORE I5-8400 CPU @ 2.80GHZ 6 13,235 79,410 Intel
33 CORE I7-6700K CPU @ 4.00GHZ 8 9,427 75,416 Intel
34 CORE I5-8600T CPU @ 2.30GHZ 6 12,268 73,608 Intel
35 CORE I7-6700 CPU @ 3.40GHZ 8 8,576 68,608 Intel
36 11TH GEN CORE I5-1135G7 @ 2.40GHZ 8 7,681 61,448 Intel
37 RYZEN 7 4700U 8 7,638 61,104 AMD
38 CORE I7-4790 CPU @ 3.60GHZ 8 7,475 59,800 Intel
39 CORE I9-8950HK CPU @ 2.90GHZ 12 4,979 59,748 Intel
40 CORE I7-4770HQ CPU @ 2.20GHZ 8 7,248 57,984 Intel
41 CORE I7-4770K CPU @ 3.50GHZ 8 7,187 57,496 Intel
42 XEON CPU E3-1275 V2 @ 3.50GHZ 8 6,836 54,688 Intel
43 XEON CPU E3-1240 V2 @ 3.40GHZ 8 6,061 48,488 Intel
44 XEON CPU E31245 @ 3.30GHZ 8 4,505 36,040 Intel
45 XEON CPU E5-2620 0 @ 2.00GHZ 12 2,577 30,924 Intel