PROJECT #18415 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 Friday, 03 February 2023 06:15:10

Rank
Project
Model Name
Folding@Home Identifier
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GPU
Model
PPD
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PROJECT FOLDING PPD AVERAGES BY CPU BETA

PPDDB data as of Friday, 03 February 2023 06:15:11

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 CORE I9-8950HK CPU @ 2.90GHZ 12 211,342 2,536,104 Intel
2 RYZEN 7 5800X 8-CORE 16 44,327 709,232 AMD
3 RYZEN 9 5950X 16-CORE 32 19,613 627,616 AMD
4 RYZEN 9 7900X 12-CORE 24 23,976 575,424 AMD
5 RYZEN 7 5800X3D 8-CORE 16 32,798 524,768 AMD
6 RYZEN 9 3950X 16-CORE 32 15,063 482,016 AMD
7 RYZEN 7 7700X 8-CORE 16 28,777 460,432 AMD
8 12TH GEN CORE I9-12900K 24 18,233 437,592 Intel
9 12TH GEN CORE I7-12700K 20 21,130 422,600 Intel
10 RYZEN 7 5700X 8-CORE 16 24,702 395,232 AMD
11 RYZEN 9 5900X 12-CORE 24 14,917 358,008 AMD
12 11TH GEN CORE I7-11700K @ 3.60GHZ 16 21,766 348,256 Intel
13 11TH GEN CORE I9-11900K @ 3.50GHZ 16 21,597 345,552 Intel
14 12TH GEN CORE I5-12600K 16 19,341 309,456 Intel
15 RYZEN 9 3900XT 12-CORE 24 12,464 299,136 AMD
16 RYZEN 7 3800X 8-CORE 16 17,765 284,240 AMD
17 RYZEN 9 3900X 12-CORE 24 11,265 270,360 AMD
18 RYZEN 7 5700G 16 16,060 256,960 AMD
19 RYZEN THREADRIPPER 2970WX 24-CORE 48 5,346 256,608 AMD
20 XEON CPU E5-2690 V4 @ 2.60GHZ 28 8,396 235,088 Intel
21 CORE I9-10900X CPU @ 3.70GHZ 20 11,564 231,280 Intel
22 12TH GEN CORE I5-12400 12 18,474 221,688 Intel
23 CORE I5-9300H CPU @ 2.40GHZ 8 25,664 205,312 Intel
24 RYZEN 9 5900HS 16 12,709 203,344 AMD
25 XEON CPU E5-2680 V2 @ 2.80GHZ 40 5,006 200,240 Intel
26 CORE I7-9700K CPU @ 3.60GHZ 8 24,884 199,072 Intel
27 CORE I7-8700 CPU @ 3.20GHZ 12 16,527 198,324 Intel
28 RYZEN 9 5900 12-CORE 24 8,123 194,952 AMD
29 CORE I9-9900K CPU @ 3.60GHZ 16 11,639 186,224 Intel
30 RYZEN 5 5600X 6-CORE 12 14,459 173,508 AMD
31 RYZEN 5 3600 6-CORE 12 13,989 167,868 AMD
32 XEON CPU E5-2698 V4 @ 2.20GHZ 16 10,395 166,320 Intel
33 RYZEN 5 2600X SIX-CORE 12 13,810 165,720 AMD
34 RYZEN 7 PRO 4750G 16 10,239 163,824 AMD
35 CORE I5-10600 CPU @ 3.30GHZ 12 13,600 163,200 Intel
36 CORE I9-9900 CPU @ 3.10GHZ 16 10,091 161,456 Intel
37 XEON CPU E5-2680 V3 @ 2.50GHZ 24 6,498 155,952 Intel
38 RYZEN 7 4800H 16 9,698 155,168 AMD
39 RYZEN 5 5600G 12 12,798 153,576 AMD
40 12TH GEN CORE I9-12900H 20 7,613 152,260 Intel
41 RYZEN THREADRIPPER 3960X 24-CORE 48 3,130 150,240 AMD
42 12TH GEN CORE I3-12100F 8 18,692 149,536 Intel
43 XEON CPU E5-2697 V2 @ 2.70GHZ 24 5,775 138,600 Intel
44 RYZEN 7 3700X 8-CORE 16 8,099 129,584 AMD
45 11TH GEN CORE I7-11850H @ 2.50GHZ 16 7,210 115,360 Intel
46 CORE I7-7700K CPU @ 4.20GHZ 8 13,489 107,912 Intel
47 XEON CPU E5-2670 0 @ 2.60GHZ 32 3,059 97,888 Intel
48 11TH GEN CORE I5-11400 @ 2.60GHZ 12 7,969 95,628 Intel
49 XEON CPU E5-2650 V2 @ 2.60GHZ 32 2,965 94,880 Intel
50 11TH GEN CORE I7-11800H @ 2.30GHZ 16 5,581 89,296 Intel
51 11TH GEN CORE I9-11900F @ 2.50GHZ 16 5,529 88,464 Intel
52 APPLE M1 MAX 10 8,794 87,940 Apple
53 RYZEN 5 1600 SIX-CORE 12 7,123 85,476 AMD
54 APPLE M1 8 10,495 83,960 Apple
55 CORE I5-10400 CPU @ 2.90GHZ 12 6,834 82,008 Intel
56 CORE I7-8705G CPU @ 3.10GHZ 8 10,234 81,872 Intel
57 CORE I7-10700T CPU @ 2.00GHZ 16 5,045 80,720 Intel
58 CORE I7-9700 CPU @ 3.00GHZ 8 9,086 72,688 Intel
59 EPYC 7251 8-CORE 16 4,136 66,176 AMD
60 XEON CPU E5-2680 0 @ 2.70GHZ 16 4,077 65,232 Intel
61 CORE I5-8600T CPU @ 2.30GHZ 6 10,617 63,702 Intel
62 XEON CPU E5-1630 V3 @ 3.70GHZ 8 7,806 62,448 Intel
63 CORE I7-6700 CPU @ 3.40GHZ 8 7,787 62,296 Intel
64 CORE I7-6700K CPU @ 4.00GHZ 8 7,691 61,528 Intel
65 CORE I7-6700HQ CPU @ 2.60GHZ 8 7,648 61,184 Intel
66 RYZEN 7 2700X EIGHT-CORE 16 3,778 60,448 AMD
67 CORE I7-4790T CPU @ 2.70GHZ 8 7,243 57,944 Intel
68 XEON W-10855M CPU @ 2.80GHZ 12 4,420 53,040 Intel
69 CORE I7-4770HQ CPU @ 2.20GHZ 8 6,359 50,872 Intel
70 CORE I5-4590 CPU @ 3.30GHZ 4 12,580 50,320 Intel
71 CORE I7-3770 CPU @ 3.40GHZ 8 6,152 49,216 Intel
72 CORE I7-4770K CPU @ 3.50GHZ 8 5,892 47,136 Intel
73 11TH GEN CORE I5-1135G7 @ 2.40GHZ 8 5,754 46,032 Intel
74 CORE I5-8350U CPU @ 1.70GHZ 8 5,455 43,640 Intel
75 CORE I7-2600 CPU @ 3.40GHZ 8 5,339 42,712 Intel
76 CORE I5-8259U CPU @ 2.30GHZ 8 5,286 42,288 Intel
77 CORE I7-4700MQ CPU @ 2.40GHZ 8 5,117 40,936 Intel
78 XEON CPU E3-1240 V2 @ 3.40GHZ 8 4,995 39,960 Intel
79 11TH GEN CORE I7-1185G7 @ 3.00GHZ 8 4,754 38,032 Intel
80 XEON CPU E3-1245 V2 @ 3.40GHZ 8 4,188 33,504 Intel
81 XEON CPU E31245 @ 3.30GHZ 8 4,063 32,504 Intel
82 12TH GEN CORE I7-12700 20 1,560 31,200 Intel
83 12TH GEN CORE I7-12700KF 20 1,533 30,660 Intel
84 11TH GEN CORE I7-1165G7 @ 2.80GHZ 8 3,669 29,352 Intel
85 CORE I7-7700HQ CPU @ 2.80GHZ 8 3,412 27,296 Intel
86 CORE I5-10210U CPU @ 1.60GHZ 7 3,746 26,222 Intel
87 XEON CPU E5-2620 0 @ 2.00GHZ 12 2,120 25,440 Intel
88 RYZEN 7 3700U 8 3,122 24,976 AMD