PROJECT #18406 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: 0xa8

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

PPDDB data as of Sunday, 04 December 2022 18:13:20

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 Sunday, 04 December 2022 18:13:20

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 28,018 896,576 AMD
2 RYZEN 7 5800X 8-CORE 16 45,793 732,688 AMD
3 RYZEN 7 5800X3D 8-CORE 16 42,488 679,808 AMD
4 RYZEN 7 7700X 8-CORE 16 40,836 653,376 AMD
5 12TH GEN CORE I7-12700K 20 31,510 630,200 Intel
6 RYZEN 9 5950X 16-CORE 32 18,674 597,568 AMD
7 12TH GEN CORE I9-12900K 24 22,381 537,144 Intel
8 RYZEN 9 3900 12-CORE 24 22,171 532,104 AMD
9 RYZEN 7 5700G 16 32,839 525,424 AMD
10 RYZEN 9 5900X 12-CORE 24 19,052 457,248 AMD
11 RYZEN 7 5700X 8-CORE 16 27,472 439,552 AMD
12 11TH GEN CORE I9-11900K @ 3.50GHZ 16 26,272 420,352 Intel
13 RYZEN 9 3900XT 12-CORE 24 14,713 353,112 AMD
14 CORE I9-10900X CPU @ 3.70GHZ 20 16,233 324,660 Intel
15 RYZEN 7 3800X 8-CORE 16 20,068 321,088 AMD
16 RYZEN THREADRIPPER 1950X 16-CORE 32 9,932 317,824 AMD
17 11TH GEN CORE I7-11700K @ 3.60GHZ 16 18,751 300,016 Intel
18 RYZEN 9 3900X 12-CORE 24 12,295 295,080 AMD
19 CORE I9-10850K CPU @ 3.60GHZ 20 14,729 294,580 Intel
20 RYZEN 7 5800H 16 16,100 257,600 AMD
21 RYZEN 5 5600G 12 21,286 255,432 AMD
22 CORE I7-8700 CPU @ 3.20GHZ 12 20,085 241,020 Intel
23 RYZEN 9 5900HS 16 14,057 224,912 AMD
24 CORE I9-9900K CPU @ 3.60GHZ 16 13,488 215,808 Intel
25 CORE I7-9700K CPU @ 3.60GHZ 8 26,883 215,064 Intel
26 RYZEN 5 5600X 6-CORE 12 16,922 203,064 AMD
27 RYZEN 5 3600 6-CORE 12 16,461 197,532 AMD
28 CORE I9-9900 CPU @ 3.10GHZ 16 12,117 193,872 Intel
29 XEON CPU E5-2690 V4 @ 2.60GHZ 28 6,817 190,876 Intel
30 XEON CPU E5-2680 V3 @ 2.50GHZ 24 7,904 189,696 Intel
31 RYZEN 7 PRO 4750G 16 11,821 189,136 AMD
32 RYZEN 7 1700 EIGHT-CORE 16 11,717 187,472 AMD
33 RYZEN THREADRIPPER 3960X 24-CORE 48 3,623 173,904 AMD
34 RYZEN 5 2600X SIX-CORE 12 13,515 162,180 AMD
35 XEON CPU E5-2698 V4 @ 2.20GHZ 16 9,494 151,904 Intel
36 RYZEN 7 3700X 8-CORE 16 9,013 144,208 AMD
37 XEON CPU E5-2650 V2 @ 2.60GHZ 32 4,155 132,960 Intel
38 CORE I7-7700K CPU @ 4.20GHZ 8 16,495 131,960 Intel
39 CORE I7-9700 CPU @ 3.00GHZ 8 16,448 131,584 Intel
40 CORE I7-5820K CPU @ 3.30GHZ 12 10,030 120,360 Intel
41 CORE I7-10700T CPU @ 2.00GHZ 16 7,079 113,264 Intel
42 APPLE M1 MAX 10 10,852 108,520 Apple
43 RYZEN 5 1600 SIX-CORE 12 7,271 87,252 AMD
44 XEON CPU E3-1270 V5 @ 3.60GHZ 8 10,498 83,984 Intel
45 CORE I5-8400 CPU @ 2.80GHZ 6 13,235 79,410 Intel
46 CORE I7-6700K CPU @ 4.00GHZ 8 9,427 75,416 Intel
47 CORE I5-8600T CPU @ 2.30GHZ 6 12,268 73,608 Intel
48 APPLE M1 8 8,858 70,864 Apple
49 XEON CPU E5-2680 0 @ 2.70GHZ 16 4,414 70,624 Intel
50 CORE I7-6700 CPU @ 3.40GHZ 8 8,576 68,608 Intel
51 11TH GEN CORE I5-1135G7 @ 2.40GHZ 8 7,681 61,448 Intel
52 RYZEN 7 4700U 8 7,638 61,104 AMD
53 CORE I7-4790 CPU @ 3.60GHZ 8 7,475 59,800 Intel
54 CORE I9-8950HK CPU @ 2.90GHZ 12 4,979 59,748 Intel
55 CORE I7-4770HQ CPU @ 2.20GHZ 8 7,248 57,984 Intel
56 CORE I7-4770K CPU @ 3.50GHZ 8 7,187 57,496 Intel
57 XEON CPU E3-1275 V2 @ 3.50GHZ 8 6,836 54,688 Intel
58 CORE I7-7700HQ CPU @ 2.80GHZ 8 6,196 49,568 Intel
59 XEON CPU E3-1240 V2 @ 3.40GHZ 8 6,061 48,488 Intel
60 APPLE M1 PRO 10 4,844 48,440 Apple
61 XEON CPU E31245 @ 3.30GHZ 8 4,505 36,040 Intel
62 XEON CPU E5-2620 0 @ 2.00GHZ 12 2,577 30,924 Intel
63 CORE I5-10210U CPU @ 1.60GHZ 7 4,108 28,756 Intel