PROJECT #18417 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 42,741 683,856 AMD
2 RYZEN 9 7950X 16-CORE 32 20,235 647,520 AMD
3 RYZEN 7 7700X 8-CORE 16 37,311 596,976 AMD
4 RYZEN 7 5800X3D 8-CORE 16 37,281 596,496 AMD
5 RYZEN 9 5950X 16-CORE 32 18,234 583,488 AMD
6 RYZEN 9 5900X 12-CORE 24 20,768 498,432 AMD
7 12TH GEN CORE I9-12900K 24 18,729 449,496 Intel
8 RYZEN 7 5700X 8-CORE 16 25,717 411,472 AMD
9 11TH GEN CORE I9-11900K @ 3.50GHZ 16 22,280 356,480 Intel
10 RYZEN 9 3950X 16-CORE 32 10,615 339,680 AMD
11 RYZEN 7 5700G 16 20,726 331,616 AMD
12 11TH GEN CORE I7-11700K @ 3.60GHZ 16 20,166 322,656 Intel
13 RYZEN 9 3900XT 12-CORE 24 13,123 314,952 AMD
14 RYZEN THREADRIPPER 1950X 16-CORE 32 8,965 286,880 AMD
15 XEON SILVER 4208 CPU @ 2.10GHZ 32 8,891 284,512 Intel
16 RYZEN 9 3900X 12-CORE 24 11,309 271,416 AMD
17 CORE I9-10850K CPU @ 3.60GHZ 20 12,881 257,620 Intel
18 RYZEN 7 3800X 8-CORE 16 15,891 254,256 AMD
19 RYZEN 5 5600X 6-CORE 12 20,657 247,884 AMD
20 RYZEN THREADRIPPER 2950X 16-CORE 32 6,656 212,992 AMD
21 RYZEN 9 5900HS 16 13,078 209,248 AMD
22 12TH GEN CORE I5-12600K 16 11,761 188,176 Intel
23 XEON CPU E5-2690 V4 @ 2.60GHZ 28 6,474 181,272 Intel
24 RYZEN 7 2700X EIGHT-CORE 16 11,217 179,472 AMD
25 CORE I9-9900K CPU @ 3.60GHZ 16 11,145 178,320 Intel
26 RYZEN 5 5600G 12 14,676 176,112 AMD
27 CORE I7-9750H CPU @ 2.60GHZ 12 14,529 174,348 Intel
28 CORE I9-7940X CPU @ 3.10GHZ 28 6,064 169,792 Intel
29 APPLE M1 MAX 10 16,715 167,150 Apple
30 RYZEN 7 PRO 4750G 16 10,426 166,816 AMD
31 CORE I9-9900 CPU @ 3.10GHZ 16 10,154 162,464 Intel
32 XEON CPU E5-2680 V3 @ 2.50GHZ 24 6,658 159,792 Intel
33 CORE I7-8700 CPU @ 3.20GHZ 12 13,175 158,100 Intel
34 RYZEN 5 3600 6-CORE 12 12,975 155,700 AMD
35 RYZEN 5 2600X SIX-CORE 12 12,926 155,112 AMD
36 RYZEN 7 5800H 16 9,608 153,728 AMD
37 RYZEN 5 3500 6-CORE 6 24,142 144,852 AMD
38 RYZEN 7 3700X 8-CORE 16 8,296 132,736 AMD
39 XEON CPU E5-2698 V4 @ 2.20GHZ 16 8,252 132,032 Intel
40 CORE I7-7700K CPU @ 4.20GHZ 8 14,250 114,000 Intel
41 CORE I7-9700K CPU @ 3.60GHZ 8 13,669 109,352 Intel
42 11TH GEN CORE I5-11400 @ 2.60GHZ 12 9,035 108,420 Intel
43 CORE I5-8400 CPU @ 2.80GHZ 6 17,125 102,750 Intel
44 XEON CPU E5-2650 V2 @ 2.60GHZ 32 3,139 100,448 Intel
45 RYZEN 5 2600 SIX-CORE 12 8,037 96,444 AMD
46 CORE I7-5820K CPU @ 3.30GHZ 12 7,717 92,604 Intel
47 CORE I7-10700T CPU @ 2.00GHZ 16 5,395 86,320 Intel
48 CORE I7-10750H CPU @ 2.60GHZ 12 6,996 83,952 Intel
49 XEON CPU E5-2670 0 @ 2.60GHZ 32 2,507 80,224 Intel
50 CORE I7-8705G CPU @ 3.10GHZ 8 9,914 79,312 Intel
51 RYZEN 5 1600 SIX-CORE 12 6,312 75,744 AMD
52 CORE I9-8950HK CPU @ 2.90GHZ 12 6,217 74,604 Intel
53 11TH GEN CORE I7-11370H @ 3.30GHZ 8 9,313 74,504 Intel
54 XEON CPU E3-1270 V5 @ 3.60GHZ 8 9,213 73,704 Intel
55 CORE I5-8600T CPU @ 2.30GHZ 6 11,963 71,778 Intel
56 APPLE M1 8 8,271 66,168 Apple
57 CORE I7-6700K CPU @ 4.00GHZ 8 7,998 63,984 Intel
58 XEON CPU E5-1630 V3 @ 3.70GHZ 8 7,692 61,536 Intel
59 CORE I7-10510U CPU @ 1.80GHZ 8 6,947 55,576 Intel
60 CORE I5-8259U CPU @ 2.30GHZ 8 6,365 50,920 Intel
61 XEON CPU E5-2680 0 @ 2.70GHZ 16 3,108 49,728 Intel
62 CORE I7-4790T CPU @ 2.70GHZ 8 6,164 49,312 Intel
63 CORE I7-3770 CPU @ 3.40GHZ 8 6,074 48,592 Intel
64 RYZEN 5 2400G 8 5,971 47,768 AMD
65 CORE I7-4770HQ CPU @ 2.20GHZ 8 5,903 47,224 Intel
66 APPLE M1 PRO 10 4,673 46,730 Apple
67 XEON CPU E5-2697 V2 @ 2.70GHZ 24 1,940 46,560 Intel
68 CORE I7-4770 CPU @ 3.40GHZ 8 5,673 45,384 Intel
69 XEON CPU E3-1240 V2 @ 3.40GHZ 8 5,277 42,216 Intel
70 11TH GEN CORE I5-1135G7 @ 2.40GHZ 8 4,997 39,976 Intel
71 XEON CPU E3-1245 V2 @ 3.40GHZ 8 4,634 37,072 Intel
72 CORE I7-7700HQ CPU @ 2.80GHZ 8 4,623 36,984 Intel
73 XEON CPU E31245 @ 3.30GHZ 8 4,381 35,048 Intel
74 RYZEN 7 4700U 8 4,351 34,808 AMD
75 RYZEN 5 PRO 2400G 8 4,280 34,240 AMD
76 RYZEN 5 3500U 8 3,961 31,688 AMD
77 CORE I7 CPU 975 @ 3.33GHZ 8 3,473 27,784 Intel
78 CORE I7-3770K CPU @ 3.50GHZ 8 3,332 26,656 Intel
79 11TH GEN CORE I3-1125G4 @ 2.00GHZ 8 3,032 24,256 Intel
80 CORE I7-2760QM CPU @ 2.40GHZ 8 2,651 21,208 Intel