PROJECT #18414 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 Saturday, 28 January 2023 00:14:36

Rank
Project
Model Name
Folding@Home Identifier
Make
Brand
GPU
Model
PPD
Average
Points WU
Average
WUs Day
Average
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PROJECT FOLDING PPD AVERAGES BY CPU BETA

PPDDB data as of Saturday, 28 January 2023 00:14:36

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 CORE I5-8365U CPU @ 1.60GHZ 8 235,865 1,886,920 Intel
2 RYZEN 7 5800X 8-CORE 16 45,350 725,600 AMD
3 RYZEN 9 7900X 12-CORE 24 27,653 663,672 AMD
4 RYZEN 7 5800X3D 8-CORE 16 40,409 646,544 AMD
5 12TH GEN CORE I9-12900K 24 22,254 534,096 Intel
6 RYZEN 9 5950X 16-CORE 32 15,361 491,552 AMD
7 12TH GEN CORE I7-12700K 20 23,581 471,620 Intel
8 RYZEN 9 5900X 12-CORE 24 19,038 456,912 AMD
9 CORE I9-9900X CPU @ 3.50GHZ 20 22,796 455,920 Intel
10 RYZEN 7 5700X 8-CORE 16 25,784 412,544 AMD
11 RYZEN 7 5700G 16 24,922 398,752 AMD
12 RYZEN 9 3950X 16-CORE 32 12,018 384,576 AMD
13 11TH GEN CORE I9-11900K @ 3.50GHZ 16 22,748 363,968 Intel
14 RYZEN 9 3900XT 12-CORE 24 13,949 334,776 AMD
15 12TH GEN CORE I7-12700 20 15,189 303,780 Intel
16 RYZEN THREADRIPPER 2950X 16-CORE 32 9,240 295,680 AMD
17 12TH GEN CORE I5-12600K 16 17,914 286,624 Intel
18 RYZEN 7 3800X 8-CORE 16 17,782 284,512 AMD
19 CORE I7-10870H CPU @ 2.20GHZ 16 15,997 255,952 Intel
20 RYZEN 9 3900X 12-CORE 24 10,455 250,920 AMD
21 CORE I9-10900X CPU @ 3.70GHZ 20 12,493 249,860 Intel
22 RYZEN 5 5600G 12 19,273 231,276 AMD
23 XEON CPU E5-2690 V4 @ 2.60GHZ 28 7,904 221,312 Intel
24 XEON W-2175 CPU @ 2.50GHZ 28 7,761 217,308 Intel
25 RYZEN 9 5900HS 16 13,346 213,536 AMD
26 RYZEN 5 5600X 6-CORE 12 17,510 210,120 AMD
27 APPLE M1 MAX 10 20,690 206,900 Apple
28 RYZEN 7 5800H 16 12,538 200,608 AMD
29 11TH GEN CORE I7-11800H @ 2.30GHZ 16 12,057 192,912 Intel
30 CORE I7-8700 CPU @ 3.20GHZ 12 15,342 184,104 Intel
31 XEON CPU E5-2698 V4 @ 2.20GHZ 16 11,407 182,512 Intel
32 CORE I7-5960X CPU @ 3.00GHZ 16 11,150 178,400 Intel
33 RYZEN 7 3700X 8-CORE 16 10,962 175,392 AMD
34 RYZEN 7 2700X EIGHT-CORE 16 10,655 170,480 AMD
35 CORE I7-9700K CPU @ 3.60GHZ 8 20,920 167,360 Intel
36 CORE I9-9900K CPU @ 3.60GHZ 16 10,456 167,296 Intel
37 XEON CPU E5-2680 V3 @ 2.50GHZ 24 6,681 160,344 Intel
38 XEON CPU E5-2665 0 @ 2.40GHZ 32 4,751 152,032 Intel
39 RYZEN 5 3500 6-CORE 6 25,197 151,182 AMD
40 RYZEN 5 3600 6-CORE 12 11,918 143,016 AMD
41 RYZEN 7 PRO 4750G 16 8,921 142,736 AMD
42 CORE I5-8400 CPU @ 2.80GHZ 6 22,997 137,982 Intel
43 XEON CPU E5-2697 V2 @ 2.70GHZ 24 5,695 136,680 Intel
44 RYZEN 5 2600X SIX-CORE 12 11,247 134,964 AMD
45 12TH GEN CORE I9-12900H 20 6,643 132,860 Intel
46 CORE I7-9700 CPU @ 3.00GHZ 8 16,160 129,280 Intel
47 RYZEN 5 3600X 6-CORE 12 10,621 127,452 AMD
48 XEON CPU E5-2650L V4 @ 1.70GHZ 28 4,254 119,112 Intel
49 CORE I7-10700F CPU @ 2.90GHZ 16 7,439 119,024 Intel
50 CORE I7-5820K CPU @ 3.30GHZ 12 9,815 117,780 Intel
51 11TH GEN CORE I5-1135G7 @ 2.40GHZ 8 13,681 109,448 Intel
52 CORE I7-7700K CPU @ 4.20GHZ 8 13,386 107,088 Intel
53 CORE I7-9750H CPU @ 2.60GHZ 12 8,761 105,132 Intel
54 CORE I7-10700 CPU @ 2.90GHZ 16 6,459 103,344 Intel
55 CORE I7-9700KF CPU @ 3.60GHZ 8 12,351 98,808 Intel
56 CORE I7-10700T CPU @ 2.00GHZ 16 5,711 91,376 Intel
57 RYZEN 5 3600XT 6-CORE 12 7,584 91,008 AMD
58 11TH GEN CORE I5-11400 @ 2.60GHZ 12 6,776 81,312 Intel
59 RYZEN 5 1600 SIX-CORE 12 6,759 81,108 AMD
60 CORE I7-8705G CPU @ 3.10GHZ 8 10,116 80,928 Intel
61 RYZEN 5 2600 SIX-CORE 12 6,509 78,108 AMD
62 XEON W-10855M CPU @ 2.80GHZ 12 5,989 71,868 Intel
63 CORE I9-8950HK CPU @ 2.90GHZ 12 5,553 66,636 Intel
64 APPLE M1 8 7,670 61,360 Apple
65 CORE I3-10100 CPU @ 3.60GHZ 8 7,341 58,728 Intel
66 XEON CPU E5-2680 0 @ 2.70GHZ 16 3,487 55,792 Intel
67 CORE I7-4790 CPU @ 3.60GHZ 8 6,609 52,872 Intel
68 CORE I5-9400F CPU @ 2.90GHZ 6 8,771 52,626 Intel
69 CORE I7-4770HQ CPU @ 2.20GHZ 8 6,480 51,840 Intel
70 CORE I7-6700K CPU @ 4.00GHZ 8 6,269 50,152 Intel
71 CORE I7-4790T CPU @ 2.70GHZ 8 5,987 47,896 Intel
72 XEON CPU E3-1240 V2 @ 3.40GHZ 8 5,833 46,664 Intel
73 CORE I7-3770 CPU @ 3.40GHZ 8 5,795 46,360 Intel
74 APPLE M1 PRO 10 4,527 45,270 Apple
75 CORE I7-4770K CPU @ 3.50GHZ 8 5,571 44,568 Intel
76 CORE I7-4770 CPU @ 3.40GHZ 8 5,464 43,712 Intel
77 CORE I7-7700HQ CPU @ 2.80GHZ 8 5,270 42,160 Intel
78 XEON CPU E5-1620 0 @ 3.60GHZ 8 5,081 40,648 Intel
79 CORE I5-8259U CPU @ 2.30GHZ 8 4,996 39,968 Intel
80 XEON CPU E3-1245 V2 @ 3.40GHZ 8 4,513 36,104 Intel
81 11TH GEN CORE I7-1165G7 @ 2.80GHZ 8 3,772 30,176 Intel
82 XEON CPU E31245 @ 3.30GHZ 8 3,521 28,168 Intel
83 11TH GEN CORE I3-1125G4 @ 2.00GHZ 8 3,224 25,792 Intel
84 CORE I7-2760QM CPU @ 2.40GHZ 8 2,955 23,640 Intel
85 CORE I7 CPU 975 @ 3.33GHZ 8 2,322 18,576 Intel