PROJECT #18418 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: 35,650

Core: 0xa8

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

PPDDB data as of Tuesday, 07 February 2023 06:14:50

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 Tuesday, 07 February 2023 06:14:50

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 RYZEN 7 5800X 8-CORE 16 40,205 643,280 AMD
2 RYZEN 9 7900X 12-CORE 24 24,125 579,000 AMD
3 RYZEN 7 7700X 8-CORE 16 33,243 531,888 AMD
4 RYZEN 7 5800X3D 8-CORE 16 32,156 514,496 AMD
5 12TH GEN CORE I9-12900K 24 17,801 427,224 Intel
6 RYZEN 9 5950X 16-CORE 32 12,871 411,872 AMD
7 RYZEN 9 3900 12-CORE 24 16,776 402,624 AMD
8 RYZEN 7 5700G 16 25,005 400,080 AMD
9 RYZEN 7 5700X 8-CORE 16 24,776 396,416 AMD
10 RYZEN 9 3950X 16-CORE 32 11,837 378,784 AMD
11 11TH GEN CORE I9-11900K @ 3.50GHZ 16 23,404 374,464 Intel
12 RYZEN 9 5900X 12-CORE 24 15,018 360,432 AMD
13 11TH GEN CORE I7-11700K @ 3.60GHZ 16 20,751 332,016 Intel
14 RYZEN THREADRIPPER 1950X 16-CORE 32 10,283 329,056 AMD
15 RYZEN 7 5800H 16 18,226 291,616 AMD
16 RYZEN 7 3800X 8-CORE 16 17,589 281,424 AMD
17 CORE I9-10850K CPU @ 3.60GHZ 20 13,033 260,660 Intel
18 12TH GEN CORE I7-12700K 20 12,944 258,880 Intel
19 RYZEN 9 5900 12-CORE 24 10,727 257,448 AMD
20 XEON CPU E5-2690 V4 @ 2.60GHZ 28 8,788 246,064 Intel
21 RYZEN 5 3600X 6-CORE 12 20,373 244,476 AMD
22 CORE I9-7920X CPU @ 2.90GHZ 24 10,132 243,168 Intel
23 RYZEN 5 5600G 12 19,997 239,964 AMD
24 CORE I9-10900X CPU @ 3.70GHZ 20 11,634 232,680 Intel
25 RYZEN 9 3900X 12-CORE 24 9,193 220,632 AMD
26 RYZEN 9 5900HS 16 13,521 216,336 AMD
27 RYZEN 9 3900XT 12-CORE 24 8,644 207,456 AMD
28 CORE I7-8700 CPU @ 3.20GHZ 12 17,174 206,088 Intel
29 RYZEN 5 5600X 6-CORE 12 17,010 204,120 AMD
30 CORE I7-9700K CPU @ 3.60GHZ 8 23,579 188,632 Intel
31 CORE I9-9900K CPU @ 3.60GHZ 16 11,788 188,608 Intel
32 XEON CPU E5-2667 V2 @ 3.30GHZ 32 5,745 183,840 Intel
33 CORE I7-4790K CPU @ 4.00GHZ 8 22,419 179,352 Intel
34 APPLE M1 MAX 10 17,684 176,840 Apple
35 CORE I7-5960X CPU @ 3.00GHZ 16 10,965 175,440 Intel
36 CORE I7-9700 CPU @ 3.00GHZ 8 21,848 174,784 Intel
37 12TH GEN CORE I5-12600K 16 10,821 173,136 Intel
38 RYZEN 7 4800H 16 10,541 168,656 AMD
39 RYZEN 5 2600X SIX-CORE 12 13,787 165,444 AMD
40 XEON CPU E5-2698 V4 @ 2.20GHZ 16 10,336 165,376 Intel
41 RYZEN 7 PRO 4750G 16 9,856 157,696 AMD
42 GENUINE CPU 0000 @ 2.60GHZ 16 9,450 151,200 Intel
43 RYZEN 5 3600 6-CORE 12 11,863 142,356 AMD
44 12TH GEN CORE I9-12900H 20 6,984 139,680 Intel
45 RYZEN 7 2700X EIGHT-CORE 16 7,989 127,824 AMD
46 11TH GEN CORE I9-11900F @ 2.50GHZ 16 7,277 116,432 Intel
47 CORE I7-7700K CPU @ 4.20GHZ 8 14,134 113,072 Intel
48 11TH GEN CORE I5-11400 @ 2.60GHZ 12 9,154 109,848 Intel
49 CORE I7-5820K CPU @ 3.30GHZ 12 9,038 108,456 Intel
50 XEON CPU E5-2650 V2 @ 2.60GHZ 32 3,180 101,760 Intel
51 CORE I7-10700T CPU @ 2.00GHZ 16 6,000 96,000 Intel
52 CORE I5-10400 CPU @ 2.90GHZ 12 7,455 89,460 Intel
53 RYZEN 5 1600 SIX-CORE 12 7,224 86,688 AMD
54 CORE I5-9400F CPU @ 2.90GHZ 6 13,659 81,954 Intel
55 RYZEN 5 2600 SIX-CORE 12 6,785 81,420 AMD
56 RYZEN 7 3700X 8-CORE 16 5,063 81,008 AMD
57 CORE I9-8950HK CPU @ 2.90GHZ 12 6,697 80,364 Intel
58 CORE I7-8705G CPU @ 3.10GHZ 8 9,976 79,808 Intel
59 CORE I7-10750H CPU @ 2.60GHZ 12 6,564 78,768 Intel
60 XEON CPU E3-1270 V5 @ 3.60GHZ 8 9,324 74,592 Intel
61 CORE I7-6700K CPU @ 4.00GHZ 8 8,903 71,224 Intel
62 CORE I7-4790 CPU @ 3.60GHZ 8 8,053 64,424 Intel
63 XEON CPU E5-1630 V3 @ 3.70GHZ 8 7,958 63,664 Intel
64 XEON CPU E5-2680 0 @ 2.70GHZ 16 3,877 62,032 Intel
65 CORE I7-6700 CPU @ 3.40GHZ 8 7,684 61,472 Intel
66 APPLE M1 8 7,627 61,016 Apple
67 CORE I5-8600T CPU @ 2.30GHZ 6 10,077 60,462 Intel
68 CORE I7-6700HQ CPU @ 2.60GHZ 8 7,527 60,216 Intel
69 RYZEN 5 3500 6-CORE 6 9,975 59,850 AMD
70 XEON CPU X5660 @ 2.80GHZ 24 2,179 52,296 Intel
71 APPLE M1 PRO 10 4,926 49,260 Apple
72 CORE I7-4790T CPU @ 2.70GHZ 8 6,151 49,208 Intel
73 CORE I5-1035G4 CPU @ 1.10GHZ 8 6,096 48,768 Intel
74 CORE I7-3770 CPU @ 3.40GHZ 8 5,994 47,952 Intel
75 CORE I5-4590 CPU @ 3.30GHZ 4 11,920 47,680 Intel
76 XEON CPU E5-2697 V2 @ 2.70GHZ 24 1,977 47,448 Intel
77 CORE I7-4770HQ CPU @ 2.20GHZ 8 5,875 47,000 Intel
78 CORE I3-10100 CPU @ 3.60GHZ 8 5,481 43,848 Intel
79 CORE I7-4770K CPU @ 3.50GHZ 8 5,418 43,344 Intel
80 XEON CPU E3-1240 V2 @ 3.40GHZ 8 5,359 42,872 Intel
81 CORE I5-8250U CPU @ 1.60GHZ 8 5,004 40,032 Intel
82 CORE I5-8259U CPU @ 2.30GHZ 8 4,473 35,784 Intel
83 CORE I7-7700HQ CPU @ 2.80GHZ 8 4,339 34,712 Intel
84 XEON CPU E3-1245 V2 @ 3.40GHZ 8 4,177 33,416 Intel
85 XEON CPU E31245 @ 3.30GHZ 8 3,666 29,328 Intel
86 CORE I7-2760QM CPU @ 2.40GHZ 8 2,896 23,168 Intel
87 OPTERON(TM) 6380 64 334 21,376 AMD