PROJECT #18411 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: 0xa8

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

PPDDB data as of Tuesday, 07 February 2023 06:14:50

Rank
Project
Model Name
Folding@Home Identifier
Make
Brand
GPU
Model
PPD
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PROJECT FOLDING PPD AVERAGES BY CPU BETA

PPDDB data as of Tuesday, 07 February 2023 06:14:50

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 RYZEN 7 7700X 8-CORE 16 38,492 615,872 AMD
2 RYZEN 9 7900X 12-CORE 24 25,505 612,120 AMD
3 RYZEN 9 3950X 16-CORE 32 18,195 582,240 AMD
4 12TH GEN CORE I9-12900K 24 23,330 559,920 Intel
5 RYZEN 9 5950X 16-CORE 32 16,199 518,368 AMD
6 12TH GEN CORE I7-12700K 20 24,670 493,400 Intel
7 RYZEN 7 5800X 8-CORE 16 28,344 453,504 AMD
8 RYZEN 7 5700X 8-CORE 16 27,999 447,984 AMD
9 RYZEN 7 5800X3D 8-CORE 16 27,309 436,944 AMD
10 CORE I9-10920X CPU @ 3.50GHZ 24 16,210 389,040 Intel
11 CORE I9-10850K CPU @ 3.60GHZ 20 19,441 388,820 Intel
12 12TH GEN CORE I7-12700 20 19,110 382,200 Intel
13 11TH GEN CORE I7-11700K @ 3.60GHZ 16 23,767 380,272 Intel
14 RYZEN 9 5900X 12-CORE 24 15,624 374,976 AMD
15 RYZEN 9 3900 12-CORE 24 15,473 371,352 AMD
16 RYZEN 9 3900XT 12-CORE 24 14,372 344,928 AMD
17 XEON CPU E5-2690 V4 @ 2.60GHZ 28 11,702 327,656 Intel
18 11TH GEN CORE I9-11900K @ 3.50GHZ 16 20,271 324,336 Intel
19 12TH GEN CORE I5-12400 12 26,779 321,348 Intel
20 XEON CPU E5-2680 V4 @ 2.40GHZ 28 11,471 321,188 Intel
21 RYZEN 9 3900X 12-CORE 24 12,462 299,088 AMD
22 XEON CPU E5-2680 V2 @ 2.80GHZ 40 7,090 283,600 Intel
23 CORE I9-9900K CPU @ 3.60GHZ 16 16,358 261,728 Intel
24 RYZEN 7 3800X 8-CORE 16 16,337 261,392 AMD
25 12TH GEN CORE I9-12900H 20 12,684 253,680 Intel
26 GENUINE 0000 @ 1.80GHZ 16 14,423 230,768 Intel
27 XEON CPU E5-2680 V3 @ 2.50GHZ 24 9,133 219,192 Intel
28 RYZEN THREADRIPPER 2950X 16-CORE 32 6,047 193,504 AMD
29 XEON CPU E5-2698 V4 @ 2.20GHZ 16 11,097 177,552 Intel
30 RYZEN 7 PRO 4750G 16 10,544 168,704 AMD
31 XEON CPU E5-2665 0 @ 2.40GHZ 32 5,169 165,408 Intel
32 RYZEN THREADRIPPER 1920X 12-CORE 24 6,690 160,560 AMD
33 RYZEN 7 3700X 8-CORE 16 9,902 158,432 AMD
34 CORE I7-10700K CPU @ 3.80GHZ 16 9,251 148,016 Intel
35 XEON CPU E5-2650L V4 @ 1.70GHZ 28 4,578 128,184 Intel
36 CORE I7-10700T CPU @ 2.00GHZ 16 6,738 107,808 Intel
37 EPYC 7251 8-CORE 16 6,596 105,536 AMD
38 CORE I9-9880H CPU @ 2.30GHZ 16 6,523 104,368 Intel
39 XEON CPU E5-2680 0 @ 2.70GHZ 16 4,687 74,992 Intel
40 RYZEN 7 2700X EIGHT-CORE 16 4,570 73,120 AMD
41 RYZEN 9 5900HX 16 4,254 68,064 AMD
42 XEON CPU E5-2697 V2 @ 2.70GHZ 24 2,710 65,040 Intel
43 11TH GEN CORE I7-11800H @ 2.30GHZ 16 3,920 62,720 Intel