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.

.

PROJECT INFO

Manager(s): Prof. Vincent Voelz

Institution: Temple University

PROJECT WORK UNIT SUMMARY

Atoms: 64,500

Core: 0xa8

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

PPDDB data as of Friday, 03 February 2023 06:15:11

Rank
Project
Model Name
Folding@Home Identifier
Make
Brand
GPU
Model
PPD
Average
Points WU
Average
WUs Day
Average
WU Time
Average

PROJECT FOLDING PPD AVERAGES BY CPU BETA

PPDDB data as of Friday, 03 February 2023 06:15:11

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 RYZEN 9 7950X 16-CORE 32 24,873 795,936 AMD
2 RYZEN 7 7700X 8-CORE 16 39,156 626,496 AMD
3 RYZEN 9 5950X 16-CORE 32 19,071 610,272 AMD
4 RYZEN 9 3950X 16-CORE 32 18,980 607,360 AMD
5 12TH GEN CORE I9-12900K 24 23,599 566,376 Intel
6 RYZEN 7 5800X3D 8-CORE 16 35,013 560,208 AMD
7 RYZEN 9 5900X 12-CORE 24 21,778 522,672 AMD
8 RYZEN 7 5800X 8-CORE 16 29,961 479,376 AMD
9 CORE I7-10700K CPU @ 3.80GHZ 16 28,831 461,296 Intel
10 RYZEN 9 3900 12-CORE 24 18,770 450,480 AMD
11 RYZEN 7 5700X 8-CORE 16 28,075 449,200 AMD
12 RYZEN THREADRIPPER 1950X 16-CORE 32 13,520 432,640 AMD
13 XEON CPU E5-2680 V4 @ 2.40GHZ 28 15,008 420,224 Intel
14 12TH GEN CORE I7-12700K 20 20,314 406,280 Intel
15 11TH GEN CORE I7-11700K @ 3.60GHZ 16 25,295 404,720 Intel
16 12TH GEN CORE I7-12700 20 20,079 401,580 Intel
17 RYZEN 9 3900XT 12-CORE 24 14,449 346,776 AMD
18 EPYC 7V12 64-CORE 64 5,149 329,536 AMD
19 CORE I9-10850K CPU @ 3.60GHZ 20 16,159 323,180 Intel
20 XEON CPU E5-2690 V4 @ 2.60GHZ 28 11,315 316,820 Intel
21 RYZEN 9 3900X 12-CORE 24 13,186 316,464 AMD
22 RYZEN 9 5900 12-CORE 24 12,293 295,032 AMD
23 RYZEN 7 5800H 16 18,108 289,728 AMD
24 RYZEN 7 3800X 8-CORE 16 17,433 278,928 AMD
25 RYZEN 5 3600 6-CORE 12 23,082 276,984 AMD
26 RYZEN THREADRIPPER 2950X 16-CORE 32 8,622 275,904 AMD
27 XEON CPU E5-2680 V2 @ 2.80GHZ 40 6,687 267,480 Intel
28 11TH GEN CORE I9-11900K @ 3.50GHZ 16 16,654 266,464 Intel
29 XEON CPU E5-2680 V3 @ 2.50GHZ 24 10,820 259,680 Intel
30 RYZEN 7 5700G 16 15,458 247,328 AMD
31 CORE I9-9980XE CPU @ 3.00GHZ 36 6,158 221,688 Intel
32 CORE I9-9900K CPU @ 3.60GHZ 16 13,604 217,664 Intel
33 11TH GEN CORE I5-11400 @ 2.60GHZ 12 16,206 194,472 Intel
34 RYZEN 7 PRO 4750G 16 11,475 183,600 AMD
35 RYZEN 7 4800H 16 11,430 182,880 AMD
36 RYZEN 7 3700X 8-CORE 16 11,042 176,672 AMD
37 XEON CPU E5-2650 V2 @ 2.60GHZ 32 5,454 174,528 Intel
38 CORE I9-7940X CPU @ 3.10GHZ 28 5,513 154,364 Intel
39 XEON CPU E5-2698 V4 @ 2.20GHZ 16 8,765 140,240 Intel
40 RYZEN 7 2700X EIGHT-CORE 16 7,860 125,760 AMD
41 CORE I7-10700T CPU @ 2.00GHZ 16 6,624 105,984 Intel
42 XEON CPU E5-2680 0 @ 2.70GHZ 16 5,212 83,392 Intel
43 12TH GEN CORE I7-12700KF 20 3,495 69,900 Intel
44 XEON CPU E5-2697 V2 @ 2.70GHZ 24 2,071 49,704 Intel
45 OPTERON(TM) 6380 64 330 21,120 AMD