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: GRO_A8

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

PPDDB data as of Friday, 27 May 2022 05:13:25

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

PPDDB data as of Friday, 27 May 2022 05:13:25

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 45,968 735,488 AMD
3 RYZEN 9 5950X 16-CORE 32 15,387 492,384 AMD
4 RYZEN 9 5900X 12-CORE 24 19,973 479,352 AMD
5 CORE I9-9900X CPU @ 3.50GHZ 20 22,796 455,920 Intel
6 RYZEN 7 5700X 8-CORE 16 25,005 400,080 AMD
7 RYZEN 9 3950X 16-CORE 32 12,295 393,440 AMD
8 RYZEN 7 5700G 16 23,885 382,160 AMD
9 11TH GEN CORE I9-11900K @ 3.50GHZ 16 22,748 363,968 Intel
10 12TH GEN CORE I7-12700 20 15,189 303,780 Intel
11 RYZEN THREADRIPPER 2950X 16-CORE 32 9,240 295,680 AMD
12 RYZEN 7 3800X 8-CORE 16 17,709 283,344 AMD
13 CORE I7-10870H CPU @ 2.20GHZ 16 15,997 255,952 Intel
14 RYZEN 7 3700X 8-CORE 16 14,571 233,136 AMD
15 CORE I9-10900X CPU @ 3.70GHZ 20 11,384 227,680 Intel
16 RYZEN 5 5600X 6-CORE 12 18,640 223,680 AMD
17 XEON CPU E5-2690 V4 @ 2.60GHZ 28 7,904 221,312 Intel
18 XEON W-2175 CPU @ 2.50GHZ 28 7,761 217,308 Intel
19 CORE I9-9900K CPU @ 3.60GHZ 16 13,407 214,512 Intel
20 RYZEN 9 5900HS 16 13,346 213,536 AMD
21 RYZEN 7 5800H 16 12,141 194,256 AMD
22 RYZEN 5 2600X SIX-CORE 12 15,993 191,916 AMD
23 CORE I7-8700 CPU @ 3.20GHZ 12 15,403 184,836 Intel
24 CORE I7-5960X CPU @ 3.00GHZ 16 11,150 178,400 Intel
25 RYZEN 7 2700X EIGHT-CORE 16 10,655 170,480 AMD
26 XEON CPU E5-2680 V3 @ 2.50GHZ 24 6,681 160,344 Intel
27 RYZEN 5 5600G 12 12,715 152,580 AMD
28 RYZEN 5 3600 6-CORE 12 11,665 139,980 AMD
29 RYZEN 5 3600X 6-CORE 12 10,621 127,452 AMD
30 11TH GEN CORE I7-11800H @ 2.30GHZ 16 7,692 123,072 Intel
31 CORE I7-9700K CPU @ 3.60GHZ 8 13,850 110,800 Intel
32 CORE I7-10700 CPU @ 2.90GHZ 16 6,459 103,344 Intel
33 CORE I7-9700KF CPU @ 3.60GHZ 8 12,351 98,808 Intel
34 CORE I7-10700T CPU @ 2.00GHZ 16 5,872 93,952 Intel
35 RYZEN 5 3600XT 6-CORE 12 7,584 91,008 AMD
36 11TH GEN CORE I5-11400 @ 2.60GHZ 12 7,330 87,960 Intel
37 RYZEN 5 1600 SIX-CORE 12 6,759 81,108 AMD
38 RYZEN 5 2600 SIX-CORE 12 6,509 78,108 AMD
39 CORE I7-8705G CPU @ 3.10GHZ 8 9,412 75,296 Intel
40 XEON W-10855M CPU @ 2.80GHZ 12 5,989 71,868 Intel
41 CORE I9-8950HK CPU @ 2.90GHZ 12 5,263 63,156 Intel
42 CORE I3-10100 CPU @ 3.60GHZ 8 7,341 58,728 Intel
43 CORE I7-4770HQ CPU @ 2.20GHZ 8 6,371 50,968 Intel
44 CORE I7-4790T CPU @ 2.70GHZ 8 5,987 47,896 Intel
45 XEON CPU E3-1240 V2 @ 3.40GHZ 8 5,845 46,760 Intel
46 CORE I7-3770 CPU @ 3.40GHZ 8 5,795 46,360 Intel
47 CORE I7-4770 CPU @ 3.40GHZ 8 5,464 43,712 Intel
48 XEON CPU E5-1620 0 @ 3.60GHZ 8 5,081 40,648 Intel
49 CORE I5-8259U CPU @ 2.30GHZ 8 4,996 39,968 Intel
50 XEON CPU E3-1245 V2 @ 3.40GHZ 8 4,513 36,104 Intel
51 XEON CPU E31245 @ 3.30GHZ 8 3,521 28,168 Intel
52 CORE I7 CPU 975 @ 3.33GHZ 8 2,322 18,576 Intel