PROJECT #18410 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 Friday, 03 February 2023 06:15:11

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Project
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 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 13TH GEN CORE I9-13900KS 32 25,996 831,872 Intel
2 XEON CPU E5-2680 V4 @ 2.40GHZ 28 28,967 811,076 Intel
3 12TH GEN CORE I7-12700K 20 34,201 684,020 Intel
4 RYZEN 9 5950X 16-CORE 32 20,346 651,072 AMD
5 RYZEN THREADRIPPER PRO 5965WX 24-CORES 48 12,927 620,496 AMD
6 RYZEN 7 7700X 8-CORE 16 38,774 620,384 AMD
7 12TH GEN CORE I9-12900K 24 24,560 589,440 Intel
8 RYZEN 7 5800X3D 8-CORE 16 34,866 557,856 AMD
9 RYZEN 9 3950X 16-CORE 32 17,126 548,032 AMD
10 RYZEN THREADRIPPER 1950X 16-CORE 32 14,817 474,144 AMD
11 RYZEN 7 5800X 8-CORE 16 28,793 460,688 AMD
12 RYZEN THREADRIPPER 2950X 16-CORE 32 13,322 426,304 AMD
13 RYZEN 7 5700X 8-CORE 16 25,859 413,744 AMD
14 RYZEN 9 5900X 12-CORE 24 16,573 397,752 AMD
15 RYZEN 7 5700G 16 24,715 395,440 AMD
16 12TH GEN CORE I7-12700 20 19,242 384,840 Intel
17 RYZEN 9 3900 12-CORE 24 15,963 383,112 AMD
18 11TH GEN CORE I7-11700K @ 3.60GHZ 16 23,778 380,448 Intel
19 12TH GEN CORE I5-12600K 16 22,336 357,376 Intel
20 GENUINE CPU 0000 @ 2.10GHZ 44 7,803 343,332 Intel
21 XEON CPU E5-2690 V4 @ 2.60GHZ 28 11,667 326,676 Intel
22 CORE I9-7940X CPU @ 3.10GHZ 28 11,232 314,496 Intel
23 RYZEN 9 3900X 12-CORE 24 12,898 309,552 AMD
24 RYZEN 7 3800X 8-CORE 16 19,211 307,376 AMD
25 RYZEN 9 3900XT 12-CORE 24 12,468 299,232 AMD
26 CORE I9-10850K CPU @ 3.60GHZ 20 14,448 288,960 Intel
27 CORE I7-10870H CPU @ 2.20GHZ 16 17,541 280,656 Intel
28 CORE I9-10900X CPU @ 3.70GHZ 20 13,590 271,800 Intel
29 RYZEN 5 3600 6-CORE 12 22,567 270,804 AMD
30 CORE I9-7920X CPU @ 2.90GHZ 24 10,683 256,392 Intel
31 RYZEN 5 5600G 12 21,201 254,412 AMD
32 12TH GEN CORE I9-12900H 20 12,381 247,620 Intel
33 XEON CPU E5-2680 V3 @ 2.50GHZ 24 10,237 245,688 Intel
34 RYZEN 7 5800H 16 14,419 230,704 AMD
35 CORE I9-9900K CPU @ 3.60GHZ 16 13,986 223,776 Intel
36 XEON CPU E5-2650 V2 @ 2.60GHZ 32 5,980 191,360 Intel
37 RYZEN 7 3700X 8-CORE 16 11,843 189,488 AMD
38 RYZEN 9 5900 12-CORE 24 7,381 177,144 AMD
39 RYZEN 5 5600X 6-CORE 12 13,787 165,444 AMD
40 CORE I7-10700 CPU @ 2.90GHZ 16 10,193 163,088 Intel
41 RYZEN 7 PRO 4750G 16 9,594 153,504 AMD
42 11TH GEN CORE I9-11900F @ 2.50GHZ 16 8,739 139,824 Intel
43 XEON CPU E5-2670 0 @ 2.60GHZ 32 4,252 136,064 Intel
44 CORE I7-10700T CPU @ 2.00GHZ 16 7,364 117,824 Intel
45 RYZEN 7 1700 EIGHT-CORE 16 6,331 101,296 AMD
46 XEON CPU E5-2680 0 @ 2.70GHZ 16 5,763 92,208 Intel
47 XEON CPU E5-2697 V2 @ 2.70GHZ 24 3,720 89,280 Intel
48 XEON CPU E5-2698 V4 @ 2.20GHZ 16 2,935 46,960 Intel