PROJECT #18408 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: 64,500

Core: GRO_A8

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

PPDDB data as of Monday, 23 May 2022 03:34:39

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PROJECT FOLDING PPD AVERAGES BY CPU BETA

PPDDB data as of Monday, 23 May 2022 03:34:39

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 CORE I7-10700K CPU @ 3.80GHZ 16 55,899 894,384 Intel
2 RYZEN 9 3950X 16-CORE 32 18,980 607,360 AMD
3 RYZEN 9 5950X 16-CORE 32 18,626 596,032 AMD
4 RYZEN 7 5800X 8-CORE 16 29,961 479,376 AMD
5 RYZEN 9 5900X 12-CORE 24 19,478 467,472 AMD
6 RYZEN 7 5700G 16 29,144 466,304 AMD
7 RYZEN 9 3900 12-CORE 24 18,770 450,480 AMD
8 XEON CPU E5-2680 V4 @ 2.40GHZ 28 15,008 420,224 Intel
9 12TH GEN CORE I7-12700K 20 20,314 406,280 Intel
10 12TH GEN CORE I7-12700 20 20,079 401,580 Intel
11 11TH GEN CORE I7-11700K @ 3.60GHZ 16 22,868 365,888 Intel
12 RYZEN 9 3900XT 12-CORE 24 14,449 346,776 AMD
13 CORE I9-10850K CPU @ 3.60GHZ 20 16,159 323,180 Intel
14 XEON CPU E5-2690 V4 @ 2.60GHZ 28 11,315 316,820 Intel
15 RYZEN 9 3900X 12-CORE 24 12,092 290,208 AMD
16 RYZEN 7 5800H 16 18,108 289,728 AMD
17 RYZEN 5 3600 6-CORE 12 23,365 280,380 AMD
18 RYZEN THREADRIPPER 2950X 16-CORE 32 8,622 275,904 AMD
19 RYZEN 7 3800X 8-CORE 16 17,215 275,440 AMD
20 XEON CPU E5-2680 V3 @ 2.50GHZ 24 10,820 259,680 Intel
21 CORE I9-9900K CPU @ 3.60GHZ 16 14,810 236,960 Intel
22 XEON CPU E5-2650 V2 @ 2.60GHZ 32 7,321 234,272 Intel
23 11TH GEN CORE I9-11900K @ 3.50GHZ 16 12,624 201,984 Intel
24 11TH GEN CORE I5-11400 @ 2.60GHZ 12 16,206 194,472 Intel
25 RYZEN 7 PRO 4750G 16 9,290 148,640 AMD
26 XEON CPU E5-2698 V4 @ 2.20GHZ 16 8,315 133,040 Intel
27 RYZEN 7 3700X 8-CORE 16 7,974 127,584 AMD
28 RYZEN 7 2700X EIGHT-CORE 16 7,860 125,760 AMD
29 XEON CPU E5-2680 0 @ 2.70GHZ 16 5,507 88,112 Intel
30 OPTERON(TM) 6380 64 330 21,120 AMD