PROJECT #18407 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 Monday, 27 June 2022 11:45:17

Rank
Project
Model Name
Folding@Home Identifier
Make
Brand
GPU
Model
PPD
Average
Points WU
Average
WUs Day
Average
WU Time
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PROJECT FOLDING PPD AVERAGES BY CPU BETA

PPDDB data as of Monday, 27 June 2022 11:45:17

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 30,696 982,272 AMD
2 RYZEN 7 5800X 8-CORE 16 52,083 833,328 AMD
3 RYZEN 7 5700G 16 33,427 534,832 AMD
4 12TH GEN CORE I9-12900K 24 21,810 523,440 Intel
5 RYZEN 7 5700X 8-CORE 16 31,079 497,264 AMD
6 12TH GEN CORE I7-12700K 20 24,221 484,420 Intel
7 11TH GEN CORE I9-11900K @ 3.50GHZ 16 26,363 421,808 Intel
8 CORE I9-10850K CPU @ 3.60GHZ 20 20,782 415,640 Intel
9 11TH GEN CORE I7-11700K @ 3.60GHZ 16 25,383 406,128 Intel
10 RYZEN 9 3900XT 12-CORE 24 14,707 352,968 AMD
11 RYZEN 7 3800X 8-CORE 16 21,105 337,680 AMD
12 RYZEN 9 5950X 16-CORE 32 10,052 321,664 AMD
13 CORE I9-10900X CPU @ 3.70GHZ 20 14,901 298,020 Intel
14 RYZEN 5 5600X 6-CORE 12 24,802 297,624 AMD
15 XEON CPU E5-2690 V4 @ 2.60GHZ 28 8,877 248,556 Intel
16 CORE I9-9900K CPU @ 3.60GHZ 16 15,408 246,528 Intel
17 CORE I7-10700K CPU @ 3.80GHZ 16 14,837 237,392 Intel
18 RYZEN 9 5900HS 16 14,679 234,864 AMD
19 XEON CPU E5-2680 V3 @ 2.50GHZ 24 9,782 234,768 Intel
20 CORE I7-8700 CPU @ 3.20GHZ 12 19,153 229,836 Intel
21 RYZEN 7 3700X 8-CORE 16 12,000 192,000 AMD
22 RYZEN 5 3600 6-CORE 12 15,553 186,636 AMD
23 CORE I7-9700K CPU @ 3.60GHZ 8 22,633 181,064 Intel
24 CORE I7-10700 CPU @ 2.90GHZ 16 9,607 153,712 Intel
25 GENUINE CPU 0000 @ 2.70GHZ 8 16,797 134,376 Intel
26 RYZEN 5 2600 SIX-CORE 12 8,671 104,052 AMD
27 CORE I7-4790K CPU @ 4.00GHZ 8 11,401 91,208 Intel
28 RYZEN 5 1600 SIX-CORE 12 6,982 83,784 AMD
29 CORE I7-6700K CPU @ 4.00GHZ 8 9,788 78,304 Intel
30 CORE I5-8600T CPU @ 2.30GHZ 6 12,455 74,730 Intel
31 EPYC 7251 8-CORE 16 4,618 73,888 AMD
32 XEON CPU E5-2680 0 @ 2.70GHZ 16 4,542 72,672 Intel
33 XEON W-10855M CPU @ 2.80GHZ 12 5,879 70,548 Intel
34 CORE I7-4770HQ CPU @ 2.20GHZ 8 8,064 64,512 Intel
35 11TH GEN CORE I7-1185G7 @ 3.00GHZ 8 7,815 62,520 Intel
36 XEON CPU E5-2678 V3 @ 2.50GHZ 6 10,382 62,292 Intel
37 CORE I9-8950HK CPU @ 2.90GHZ 12 5,166 61,992 Intel
38 11TH GEN CORE I5-1135G7 @ 2.40GHZ 8 7,607 60,856 Intel
39 CORE I7-4790T CPU @ 2.70GHZ 8 7,305 58,440 Intel
40 CORE I7-3770 CPU @ 3.40GHZ 8 7,108 56,864 Intel
41 XEON CPU E3-1240 V2 @ 3.40GHZ 8 6,333 50,664 Intel
42 CORE I7-4770 CPU @ 3.40GHZ 8 5,911 47,288 Intel
43 CORE I7-10610U CPU @ 1.80GHZ 8 5,880 47,040 Intel
44 11TH GEN CORE I5-1145G7 @ 2.60GHZ 8 5,613 44,904 Intel
45 CORE I7-4770K CPU @ 3.50GHZ 8 5,587 44,696 Intel
46 CORE I5-8265U CPU @ 1.60GHZ 8 4,752 38,016 Intel
47 XEON CPU E3-1245 V2 @ 3.40GHZ 8 4,240 33,920 Intel