PROJECT #18419 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 Thursday, 01 December 2022 06:13:23

Rank
Project
Model Name
Folding@Home Identifier
Make
Brand
GPU
Model
PPD
Average
Points WU
Average
WUs Day
Average
WU Time
Average

PROJECT FOLDING PPD AVERAGES BY CPU BETA

PPDDB data as of Thursday, 01 December 2022 06:13:23

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 RYZEN 9 7950X 16-CORE 32 23,673 757,536 AMD
2 RYZEN 7 5800X 8-CORE 16 42,612 681,792 AMD
3 RYZEN 9 3950X 16-CORE 32 20,605 659,360 AMD
4 RYZEN 9 5950X 16-CORE 32 20,160 645,120 AMD
5 RYZEN 7 5800X3D 8-CORE 16 38,617 617,872 AMD
6 RYZEN 9 5900X 12-CORE 24 23,666 567,984 AMD
7 RYZEN 7 2700X EIGHT-CORE 16 28,652 458,432 AMD
8 12TH GEN CORE I9-12900K 24 18,606 446,544 Intel
9 RYZEN 9 3900 12-CORE 24 18,404 441,696 AMD
10 CORE I9-9980XE CPU @ 3.00GHZ 36 10,589 381,204 Intel
11 RYZEN 7 5700X 8-CORE 16 22,985 367,760 AMD
12 12TH GEN CORE I7-12700K 20 17,460 349,200 Intel
13 11TH GEN CORE I9-11900K @ 3.50GHZ 16 21,501 344,016 Intel
14 11TH GEN CORE I7-11700K @ 3.60GHZ 16 21,493 343,888 Intel
15 RYZEN 9 3900XT 12-CORE 24 13,019 312,456 AMD
16 RYZEN 7 5700G 16 19,452 311,232 AMD
17 12TH GEN CORE I5-12600K 16 18,679 298,864 Intel
18 RYZEN 7 3800X 8-CORE 16 17,887 286,192 AMD
19 RYZEN 7 5800H 16 17,264 276,224 AMD
20 CORE I9-10900X CPU @ 3.70GHZ 20 13,449 268,980 Intel
21 RYZEN 9 3900X 12-CORE 24 10,629 255,096 AMD
22 RYZEN 9 5900HS 16 13,603 217,648 AMD
23 CORE I7-8700 CPU @ 3.20GHZ 12 17,851 214,212 Intel
24 APPLE M1 MAX 10 21,397 213,970 Apple
25 CORE I9-10850K CPU @ 3.60GHZ 20 10,681 213,620 Intel
26 CORE I7-5960X CPU @ 3.00GHZ 16 13,272 212,352 Intel
27 RYZEN 5 5600X 6-CORE 12 16,702 200,424 AMD
28 RYZEN 5 3600X 6-CORE 12 16,277 195,324 AMD
29 RYZEN 7 PRO 4750G 16 11,522 184,352 AMD
30 CORE I9-9900K CPU @ 3.60GHZ 16 11,381 182,096 Intel
31 CORE I7-9700K CPU @ 3.60GHZ 8 22,735 181,880 Intel
32 XEON CPU E5-2680 V3 @ 2.50GHZ 24 7,521 180,504 Intel
33 XEON CPU E5-2698 V4 @ 2.20GHZ 16 11,031 176,496 Intel
34 11TH GEN CORE I9-11900F @ 2.50GHZ 16 10,704 171,264 Intel
35 RYZEN 5 3600 6-CORE 12 13,896 166,752 AMD
36 11TH GEN CORE I7-1185G7 @ 3.00GHZ 8 20,661 165,288 Intel
37 CORE I7-9700 CPU @ 3.00GHZ 8 20,389 163,112 Intel
38 RYZEN 7 1700 EIGHT-CORE 16 9,831 157,296 AMD
39 CORE I5-10400 CPU @ 2.90GHZ 12 12,813 153,756 Intel
40 RYZEN 7 3700X 8-CORE 16 9,144 146,304 AMD
41 CORE I7-10700 CPU @ 2.90GHZ 16 8,024 128,384 Intel
42 12TH GEN CORE I9-12900H 20 6,201 124,020 Intel
43 XEON CPU E5-2670 0 @ 2.60GHZ 32 3,765 120,480 Intel
44 XEON GOLD 6128 CPU @ 3.40GHZ 12 9,256 111,072 Intel
45 CORE I7-7700K CPU @ 4.20GHZ 8 13,715 109,720 Intel
46 GENUINE CPU 0000 @ 2.70GHZ 8 13,489 107,912 Intel
47 11TH GEN CORE I5-11400 @ 2.60GHZ 12 8,633 103,596 Intel
48 CORE I5-8400 CPU @ 2.80GHZ 6 17,108 102,648 Intel
49 11TH GEN CORE I7-11850H @ 2.50GHZ 16 6,234 99,744 Intel
50 CORE I7-6700K CPU @ 4.00GHZ 8 11,629 93,032 Intel
51 CORE I3-10105F CPU @ 3.70GHZ 8 11,490 91,920 Intel
52 RYZEN 5 2600X SIX-CORE 12 7,458 89,496 AMD
53 CORE I9-8950HK CPU @ 2.90GHZ 12 7,258 87,096 Intel
54 CORE I7-4790K CPU @ 4.00GHZ 8 10,049 80,392 Intel
55 CORE I7-8705G CPU @ 3.10GHZ 8 9,707 77,656 Intel
56 CORE I5-8350U CPU @ 1.70GHZ 8 9,703 77,624 Intel
57 CORE I7-10700T CPU @ 2.00GHZ 16 4,727 75,632 Intel
58 RYZEN 5 1600 SIX-CORE 12 5,877 70,524 AMD
59 CORE I7-4770K CPU @ 3.50GHZ 8 8,558 68,464 Intel
60 APPLE M1 8 8,229 65,832 Apple
61 XEON CPU E5-1630 V3 @ 3.70GHZ 8 7,950 63,600 Intel
62 CORE I5-8600T CPU @ 2.30GHZ 6 10,566 63,396 Intel
63 11TH GEN CORE I5-1135G7 @ 2.40GHZ 8 7,911 63,288 Intel
64 XEON CPU E5-2680 0 @ 2.70GHZ 16 3,920 62,720 Intel
65 CORE I7-6700HQ CPU @ 2.60GHZ 8 7,705 61,640 Intel
66 RYZEN 7 4700U 8 6,954 55,632 AMD
67 XEON CPU E5-2650L V4 @ 1.70GHZ 28 1,920 53,760 Intel
68 CORE I7-4770HQ CPU @ 2.20GHZ 8 6,028 48,224 Intel
69 APPLE M1 PRO 10 4,711 47,110 Apple
70 CORE I7-5820K CPU @ 3.30GHZ 12 3,882 46,584 Intel
71 CORE I7-3770 CPU @ 3.40GHZ 8 5,708 45,664 Intel
72 CORE I7-10610U CPU @ 1.80GHZ 8 5,604 44,832 Intel
73 XEON CPU E3-1245 V2 @ 3.40GHZ 8 5,379 43,032 Intel
74 CORE I7-4765T CPU @ 2.00GHZ 8 4,732 37,856 Intel
75 XEON CPU E3-1240 V2 @ 3.40GHZ 8 4,613 36,904 Intel
76 CORE I7-7700HQ CPU @ 2.80GHZ 8 4,592 36,736 Intel
77 CORE I5-10210U CPU @ 1.60GHZ 7 5,184 36,288 Intel
78 FX-8350 EIGHT-CORE 8 3,993 31,944 AMD
79 XEON CPU E31245 @ 3.30GHZ 8 3,559 28,472 Intel
80 RYZEN 7 3700U 8 3,054 24,432 AMD
81 CORE I5-7200U CPU @ 2.50GHZ 4 5,960 23,840 Intel
82 FX-6100 SIX-CORE 6 1,643 9,858 AMD