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: GRO_A8

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

PPDDB data as of Monday, 23 May 2022 03:34:39

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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 Monday, 23 May 2022 03:34:39

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 47,921 766,736 AMD
3 RYZEN 9 5950X 16-CORE 32 20,818 666,176 AMD
4 RYZEN 9 3950X 16-CORE 32 15,063 482,016 AMD
5 RYZEN 9 5900X 12-CORE 24 16,701 400,824 AMD
6 11TH GEN CORE I9-11900K @ 3.50GHZ 16 23,426 374,816 Intel
7 RYZEN 9 3900XT 12-CORE 24 12,464 299,136 AMD
8 RYZEN 9 3900X 12-CORE 24 11,831 283,944 AMD
9 RYZEN 7 3800X 8-CORE 16 16,772 268,352 AMD
10 RYZEN THREADRIPPER 2970WX 24-CORE 48 5,346 256,608 AMD
11 XEON CPU E5-2690 V4 @ 2.60GHZ 28 8,396 235,088 Intel
12 CORE I9-10900X CPU @ 3.70GHZ 20 11,564 231,280 Intel
13 RYZEN 5 5600X 6-CORE 12 17,260 207,120 AMD
14 CORE I5-9300H CPU @ 2.40GHZ 8 25,664 205,312 Intel
15 RYZEN 9 5900HS 16 12,709 203,344 AMD
16 CORE I7-8700 CPU @ 3.20GHZ 12 16,527 198,324 Intel
17 RYZEN 5 2600X SIX-CORE 12 15,648 187,776 AMD
18 CORE I7-9700 CPU @ 3.00GHZ 8 21,722 173,776 Intel
19 CORE I5-10600 CPU @ 3.30GHZ 12 13,600 163,200 Intel
20 CORE I9-9900 CPU @ 3.10GHZ 16 10,091 161,456 Intel
21 RYZEN 7 PRO 4750G 16 10,062 160,992 AMD
22 XEON CPU E5-2680 V3 @ 2.50GHZ 24 6,498 155,952 Intel
23 RYZEN THREADRIPPER 3960X 24-CORE 48 3,130 150,240 AMD
24 12TH GEN CORE I3-12100F 8 18,692 149,536 Intel
25 RYZEN 5 3600 6-CORE 12 11,545 138,540 AMD
26 RYZEN 7 3700X 8-CORE 16 6,756 108,096 AMD
27 CORE I7-7700K CPU @ 4.20GHZ 8 12,075 96,600 Intel
28 11TH GEN CORE I5-11400 @ 2.60GHZ 12 7,866 94,392 Intel
29 11TH GEN CORE I9-11900F @ 2.50GHZ 16 5,529 88,464 Intel
30 XEON CPU E5-2680 0 @ 2.70GHZ 16 5,411 86,576 Intel
31 RYZEN 5 1600 SIX-CORE 12 7,123 85,476 AMD
32 CORE I7-6700K CPU @ 4.00GHZ 8 10,080 80,640 Intel
33 CORE I7-4770K CPU @ 3.50GHZ 8 8,781 70,248 Intel
34 EPYC 7251 8-CORE 16 4,136 66,176 AMD
35 CORE I7-6700 CPU @ 3.40GHZ 8 7,787 62,296 Intel
36 CORE I7-6700HQ CPU @ 2.60GHZ 8 7,648 61,184 Intel
37 RYZEN 7 2700X EIGHT-CORE 16 3,778 60,448 AMD
38 XEON CPU E5-2698 V4 @ 2.20GHZ 16 3,733 59,728 Intel
39 CORE I7-4790T CPU @ 2.70GHZ 8 7,243 57,944 Intel
40 XEON W-10855M CPU @ 2.80GHZ 12 4,420 53,040 Intel
41 CORE I5-4590 CPU @ 3.30GHZ 4 12,580 50,320 Intel
42 CORE I7-3770 CPU @ 3.40GHZ 8 5,971 47,768 Intel
43 CORE I7-4770HQ CPU @ 2.20GHZ 8 5,760 46,080 Intel
44 11TH GEN CORE I5-1135G7 @ 2.40GHZ 8 5,754 46,032 Intel
45 CORE I7-2600 CPU @ 3.40GHZ 8 5,339 42,712 Intel
46 CORE I5-8259U CPU @ 2.30GHZ 8 5,286 42,288 Intel
47 CORE I7-4700MQ CPU @ 2.40GHZ 8 5,117 40,936 Intel
48 XEON CPU E3-1240 V2 @ 3.40GHZ 8 4,974 39,792 Intel
49 11TH GEN CORE I7-1185G7 @ 3.00GHZ 8 4,754 38,032 Intel
50 XEON CPU E3-1245 V2 @ 3.40GHZ 8 4,188 33,504 Intel
51 XEON CPU E31245 @ 3.30GHZ 8 4,063 32,504 Intel
52 12TH GEN CORE I7-12700 20 1,560 31,200 Intel
53 XEON CPU E5-2620 0 @ 2.00GHZ 12 2,120 25,440 Intel