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: 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 29,413 941,216 AMD
2 RYZEN 9 7950X 16-CORE 32 25,741 823,712 AMD
3 RYZEN 7 5800X 8-CORE 16 49,457 791,312 AMD
4 RYZEN 7 5700G 16 33,427 534,832 AMD
5 12TH GEN CORE I9-12900K 24 21,868 524,832 Intel
6 RYZEN 7 5700X 8-CORE 16 29,836 477,376 AMD
7 12TH GEN CORE I7-12700K 20 23,687 473,740 Intel
8 RYZEN 9 5950X 16-CORE 32 14,403 460,896 AMD
9 11TH GEN CORE I9-11900K @ 3.50GHZ 16 26,363 421,808 Intel
10 11TH GEN CORE I7-11700K @ 3.60GHZ 16 24,990 399,840 Intel
11 RYZEN 7 5800X3D 8-CORE 16 23,936 382,976 AMD
12 CORE I9-10850K CPU @ 3.60GHZ 20 17,846 356,920 Intel
13 RYZEN 9 3900XT 12-CORE 24 14,707 352,968 AMD
14 RYZEN 7 3800X 8-CORE 16 21,119 337,904 AMD
15 RYZEN THREADRIPPER 1950X 16-CORE 32 10,554 337,728 AMD
16 RYZEN 9 5900X 12-CORE 24 12,878 309,072 AMD
17 12TH GEN CORE I5-12400 12 25,637 307,644 Intel
18 CORE I9-10900X CPU @ 3.70GHZ 20 14,901 298,020 Intel
19 12TH GEN CORE I5-12600K 16 16,626 266,016 Intel
20 RYZEN 9 3900X 12-CORE 24 10,790 258,960 AMD
21 XEON CPU E5-2690 V4 @ 2.60GHZ 28 8,877 248,556 Intel
22 CORE I9-9900K CPU @ 3.60GHZ 16 15,408 246,528 Intel
23 RYZEN 5 5600X 6-CORE 12 19,897 238,764 AMD
24 CORE I7-10700K CPU @ 3.80GHZ 16 14,837 237,392 Intel
25 RYZEN 9 5900HS 16 14,679 234,864 AMD
26 XEON CPU E5-2680 V3 @ 2.50GHZ 24 9,782 234,768 Intel
27 RYZEN 5 5600G 12 19,433 233,196 AMD
28 CORE I7-8700 CPU @ 3.20GHZ 12 18,735 224,820 Intel
29 RYZEN 9 5900 12-CORE 24 9,129 219,096 AMD
30 RYZEN 7 5800H 16 13,439 215,024 AMD
31 CORE I7-9700K CPU @ 3.60GHZ 8 24,992 199,936 Intel
32 RYZEN 5 3600 6-CORE 12 16,329 195,948 AMD
33 RYZEN 7 PRO 4750G 16 11,970 191,520 AMD
34 APPLE M1 MAX 10 17,298 172,980 Apple
35 12TH GEN CORE I9-12900H 20 8,014 160,280 Intel
36 CORE I7-10700 CPU @ 2.90GHZ 16 9,607 153,712 Intel
37 CORE I7-10700T CPU @ 2.00GHZ 16 9,363 149,808 Intel
38 GENUINE CPU 0000 @ 2.70GHZ 8 16,797 134,376 Intel
39 CORE I7-5820K CPU @ 3.30GHZ 12 11,083 132,996 Intel
40 RYZEN 7 3700X 8-CORE 16 8,131 130,096 AMD
41 CORE I7-9700 CPU @ 3.00GHZ 8 16,089 128,712 Intel
42 RYZEN 5 2600X SIX-CORE 12 8,969 107,628 AMD
43 CORE I7-6950X CPU @ 3.00GHZ 20 5,373 107,460 Intel
44 RYZEN 5 2600 SIX-CORE 12 8,645 103,740 AMD
45 XEON CPU E5-2650 V2 @ 2.60GHZ 32 3,238 103,616 Intel
46 RYZEN 7 2700X EIGHT-CORE 16 6,082 97,312 AMD
47 CORE I7-4790K CPU @ 4.00GHZ 8 11,401 91,208 Intel
48 XEON CPU E3-1270 V5 @ 3.60GHZ 8 10,910 87,280 Intel
49 XEON CPU E5-2670 0 @ 2.60GHZ 32 2,711 86,752 Intel
50 CORE I7-6700K CPU @ 4.00GHZ 8 10,505 84,040 Intel
51 RYZEN 5 1600 SIX-CORE 12 6,982 83,784 AMD
52 CORE I5-8350U CPU @ 1.70GHZ 8 9,603 76,824 Intel
53 APPLE M1 8 9,489 75,912 Apple
54 CORE I5-8600T CPU @ 2.30GHZ 6 12,455 74,730 Intel
55 EPYC 7251 8-CORE 16 4,618 73,888 AMD
56 XEON W-10855M CPU @ 2.80GHZ 12 5,879 70,548 Intel
57 CORE I7-4770HQ CPU @ 2.20GHZ 8 8,045 64,360 Intel
58 XEON CPU E5-2680 0 @ 2.70GHZ 16 3,963 63,408 Intel
59 11TH GEN CORE I7-1185G7 @ 3.00GHZ 8 7,815 62,520 Intel
60 XEON CPU E5-2678 V3 @ 2.50GHZ 6 10,382 62,292 Intel
61 CORE I9-8950HK CPU @ 2.90GHZ 12 5,166 61,992 Intel
62 11TH GEN CORE I5-1135G7 @ 2.40GHZ 8 7,607 60,856 Intel
63 CORE I7-4790T CPU @ 2.70GHZ 8 7,305 58,440 Intel
64 CORE I7-4770 CPU @ 3.40GHZ 8 7,206 57,648 Intel
65 CORE I7-3770 CPU @ 3.40GHZ 8 7,108 56,864 Intel
66 XEON CPU E3-1240 V2 @ 3.40GHZ 8 6,333 50,664 Intel
67 APPLE M1 PRO 10 4,852 48,520 Apple
68 CORE I7-10610U CPU @ 1.80GHZ 8 5,880 47,040 Intel
69 11TH GEN CORE I5-1145G7 @ 2.60GHZ 8 5,613 44,904 Intel
70 CORE I7-7700HQ CPU @ 2.80GHZ 8 5,609 44,872 Intel
71 CORE I7-4770K CPU @ 3.50GHZ 8 5,587 44,696 Intel
72 XEON CPU E5-2650L V4 @ 1.70GHZ 28 1,492 41,776 Intel
73 CORE I5-8265U CPU @ 1.60GHZ 8 4,752 38,016 Intel
74 XEON CPU E3-1245 V2 @ 3.40GHZ 8 4,240 33,920 Intel
75 CORE I7-2760QM CPU @ 2.40GHZ 8 3,669 29,352 Intel