PROJECT #18404 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 Sunday, 26 June 2022 09:56:59

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

PPDDB data as of Sunday, 26 June 2022 09:56:59

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 35,496 1,135,872 AMD
2 RYZEN 7 5800X 8-CORE 16 49,119 785,904 AMD
3 RYZEN 7 5700G 16 43,705 699,280 AMD
4 12TH GEN CORE I9-12900K 24 21,606 518,544 Intel
5 RYZEN 7 5700X 8-CORE 16 30,621 489,936 AMD
6 11TH GEN CORE I9-11900K @ 3.50GHZ 16 26,791 428,656 Intel
7 11TH GEN CORE I7-11700K @ 3.60GHZ 16 25,628 410,048 Intel
8 RYZEN 9 3900 12-CORE 24 15,840 380,160 AMD
9 RYZEN 9 5950X 16-CORE 32 10,288 329,216 AMD
10 RYZEN 7 3800X 8-CORE 16 19,897 318,352 AMD
11 CORE I9-10900X CPU @ 3.70GHZ 20 14,101 282,020 Intel
12 RYZEN THREADRIPPER 3960X 24-CORE 48 5,226 250,848 AMD
13 RYZEN 5 3600X 6-CORE 12 20,499 245,988 AMD
14 RYZEN 9 3900X 12-CORE 24 10,090 242,160 AMD
15 RYZEN 5 5600X 6-CORE 12 20,101 241,212 AMD
16 CORE I7-10700T CPU @ 2.00GHZ 16 14,977 239,632 Intel
17 RYZEN 9 5900HS 16 14,873 237,968 AMD
18 CORE I7-8700 CPU @ 3.20GHZ 12 19,428 233,136 Intel
19 XEON CPU E5-2690 V4 @ 2.60GHZ 28 7,192 201,376 Intel
20 CORE I7-5960X CPU @ 3.00GHZ 16 12,310 196,960 Intel
21 RYZEN 7 2700X EIGHT-CORE 16 12,218 195,488 AMD
22 XEON CPU E5-2680 V3 @ 2.50GHZ 24 8,048 193,152 Intel
23 CORE I7-9700 CPU @ 3.00GHZ 8 22,827 182,616 Intel
24 RYZEN 7 PRO 4750G 16 11,300 180,800 AMD
25 CORE I9-9900 CPU @ 3.10GHZ 16 11,163 178,608 Intel
26 RYZEN 5 3600 6-CORE 12 14,045 168,540 AMD
27 EPYC 7401P 24-CORE 48 2,931 140,688 AMD
28 RYZEN 9 3900XT 12-CORE 24 5,841 140,184 AMD
29 11TH GEN CORE I5-11400 @ 2.60GHZ 12 9,197 110,364 Intel
30 RYZEN 5 1600 SIX-CORE 12 7,817 93,804 AMD
31 CORE I7-4790K CPU @ 4.00GHZ 8 11,700 93,600 Intel
32 CORE I7-8705G CPU @ 3.10GHZ 8 10,588 84,704 Intel
33 CORE I7-6700K CPU @ 4.00GHZ 8 10,573 84,584 Intel
34 CORE I9-8950HK CPU @ 2.90GHZ 12 7,007 84,084 Intel
35 CORE I7-4770K CPU @ 3.50GHZ 8 10,066 80,528 Intel
36 11TH GEN CORE I5-1135G7 @ 2.40GHZ 8 8,703 69,624 Intel
37 CORE I3-10100 CPU @ 3.60GHZ 8 8,678 69,424 Intel
38 CORE I7-10750H CPU @ 2.60GHZ 12 5,568 66,816 Intel
39 RYZEN 7 3700X 8-CORE 16 3,793 60,688 AMD
40 CORE I7-3770 CPU @ 3.40GHZ 8 7,314 58,512 Intel
41 CORE I7-6700 CPU @ 3.40GHZ 8 6,973 55,784 Intel
42 CORE I7-4770HQ CPU @ 2.20GHZ 8 6,962 55,696 Intel
43 CORE I7-4790T CPU @ 2.70GHZ 8 6,521 52,168 Intel
44 XEON CPU E3-1240 V2 @ 3.40GHZ 8 6,049 48,392 Intel
45 CORE I5-8265U CPU @ 1.60GHZ 8 4,870 38,960 Intel
46 CORE I5-10210U CPU @ 1.60GHZ 7 5,307 37,149 Intel
47 XEON CPU E31245 @ 3.30GHZ 8 3,658 29,264 Intel
48 XEON CPU E5-2620 0 @ 2.00GHZ 12 2,366 28,392 Intel