PROJECT #18403 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 7 5800X3D 8-CORE 16 45,967 735,472 AMD
2 RYZEN 9 5900X 12-CORE 24 29,801 715,224 AMD
3 RYZEN 7 7700X 8-CORE 16 41,813 669,008 AMD
4 12TH GEN CORE I7-12700K 20 33,082 661,640 Intel
5 RYZEN 7 5800X 8-CORE 16 40,014 640,224 AMD
6 RYZEN 9 3950X 16-CORE 32 18,550 593,600 AMD
7 RYZEN 7 5700G 16 35,426 566,816 AMD
8 RYZEN 9 5950X 16-CORE 32 16,396 524,672 AMD
9 RYZEN 9 3900 12-CORE 24 21,614 518,736 AMD
10 RYZEN 7 5700X 8-CORE 16 30,804 492,864 AMD
11 CORE I9-9980XE CPU @ 3.00GHZ 36 13,126 472,536 Intel
12 11TH GEN CORE I9-11900K @ 3.50GHZ 16 26,308 420,928 Intel
13 12TH GEN CORE I7-12700 20 17,087 341,740 Intel
14 RYZEN 9 3900X 12-CORE 24 13,785 330,840 AMD
15 RYZEN 7 3800X 8-CORE 16 20,446 327,136 AMD
16 CORE I9-7920X CPU @ 2.90GHZ 24 13,494 323,856 Intel
17 CORE I9-10900X CPU @ 3.70GHZ 20 14,930 298,600 Intel
18 11TH GEN CORE I7-11700K @ 3.60GHZ 16 17,780 284,480 Intel
19 CORE I9-10850K CPU @ 3.60GHZ 20 13,692 273,840 Intel
20 CORE I7-8700 CPU @ 3.20GHZ 12 20,494 245,928 Intel
21 12TH GEN CORE I5-12600K 16 15,023 240,368 Intel
22 RYZEN 7 5800H 16 14,678 234,848 AMD
23 RYZEN 9 5900HS 16 14,336 229,376 AMD
24 CORE I7-6950X CPU @ 3.00GHZ 20 11,376 227,520 Intel
25 RYZEN THREADRIPPER 3960X 24-CORE 48 4,513 216,624 AMD
26 RYZEN 5 5600X 6-CORE 12 17,665 211,980 AMD
27 RYZEN 5 3600 6-CORE 12 17,411 208,932 AMD
28 CORE I7-9700K CPU @ 3.60GHZ 8 25,938 207,504 Intel
29 XEON CPU E5-2690 V4 @ 2.60GHZ 28 7,106 198,968 Intel
30 CORE I7-8700K CPU @ 3.70GHZ 12 16,540 198,480 Intel
31 CORE I7-10700T CPU @ 2.00GHZ 16 12,354 197,664 Intel
32 CORE I9-9900K CPU @ 3.60GHZ 16 12,003 192,048 Intel
33 XEON CPU E5-2680 V2 @ 2.80GHZ 40 4,734 189,360 Intel
34 RYZEN 7 PRO 4750G 16 11,093 177,488 AMD
35 APPLE M1 MAX 10 17,716 177,160 Apple
36 RYZEN 5 2600X SIX-CORE 12 13,790 165,480 AMD
37 XEON GOLD 6128 CPU @ 3.40GHZ 12 13,514 162,168 Intel
38 XEON CPU E5-2698 V4 @ 2.20GHZ 16 9,827 157,232 Intel
39 CORE I5-8400 CPU @ 2.80GHZ 6 25,243 151,458 Intel
40 RYZEN 7 3700X 8-CORE 16 9,364 149,824 AMD
41 CORE I5-10400 CPU @ 2.90GHZ 12 12,391 148,692 Intel
42 CORE I7-9700 CPU @ 3.00GHZ 8 18,565 148,520 Intel
43 12TH GEN CORE I9-12900H 20 7,160 143,200 Intel
44 XEON CPU E5-2650 V2 @ 2.60GHZ 32 4,180 133,760 Intel
45 RYZEN THREADRIPPER 1920X 12-CORE 24 5,546 133,104 AMD
46 RYZEN 7 4800H 16 7,128 114,048 AMD
47 11TH GEN CORE I5-11400 @ 2.60GHZ 12 9,265 111,180 Intel
48 CORE I7-5820K CPU @ 3.30GHZ 12 8,751 105,012 Intel
49 RYZEN 5 1600 SIX-CORE 12 8,158 97,896 AMD
50 RYZEN 7 2700X EIGHT-CORE 16 5,618 89,888 AMD
51 RYZEN 5 2600 SIX-CORE 12 7,243 86,916 AMD
52 CORE I7-8705G CPU @ 3.10GHZ 8 10,812 86,496 Intel
53 XEON CPU E3-1270 V5 @ 3.60GHZ 8 10,668 85,344 Intel
54 CORE I7-4790K CPU @ 4.00GHZ 8 10,619 84,952 Intel
55 CORE I9-8950HK CPU @ 2.90GHZ 12 7,050 84,600 Intel
56 CORE I7-6700K CPU @ 4.00GHZ 8 10,048 80,384 Intel
57 CORE I5-8600T CPU @ 2.30GHZ 6 12,541 75,246 Intel
58 APPLE M1 8 9,347 74,776 Apple
59 11TH GEN CORE I7-1185G7 @ 3.00GHZ 8 9,229 73,832 Intel
60 CORE I7-4770 CPU @ 3.40GHZ 8 8,560 68,480 Intel
61 CORE I5-10500T CPU @ 2.30GHZ 12 5,685 68,220 Intel
62 CORE I7-6700HQ CPU @ 2.60GHZ 8 7,363 58,904 Intel
63 11TH GEN CORE I5-1135G7 @ 2.40GHZ 8 7,160 57,280 Intel
64 CORE I5-8350U CPU @ 1.70GHZ 8 6,711 53,688 Intel
65 XEON CPU E3-1270 V2 @ 3.50GHZ 8 6,553 52,424 Intel
66 CORE I7-4770HQ CPU @ 2.20GHZ 8 6,281 50,248 Intel
67 RYZEN 5 3500 6-CORE 6 8,214 49,284 AMD
68 APPLE M1 PRO 10 4,665 46,650 Apple
69 CORE I5-8259U CPU @ 2.30GHZ 8 4,809 38,472 Intel
70 CORE I7-4800MQ CPU @ 2.70GHZ 8 4,734 37,872 Intel
71 XEON CPU E3-1245 V2 @ 3.40GHZ 8 3,946 31,568 Intel
72 XEON CPU E31245 @ 3.30GHZ 8 3,873 30,984 Intel
73 11TH GEN CORE I5-1155G7 @ 2.50GHZ 8 3,322 26,576 Intel
74 CORE I7-2760QM CPU @ 2.40GHZ 8 2,864 22,912 Intel