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: GRO_A8

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

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

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 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 RYZEN 7 5800X 8-CORE 16 44,000 704,000 AMD
2 RYZEN 9 5950X 16-CORE 32 14,079 450,528 AMD
3 RYZEN 7 5700X 8-CORE 16 26,904 430,464 AMD
4 RYZEN 9 5900X 12-CORE 24 16,188 388,512 AMD
5 11TH GEN CORE I9-11900K @ 3.50GHZ 16 22,280 356,480 Intel
6 RYZEN 9 3950X 16-CORE 32 10,615 339,680 AMD
7 RYZEN 7 5700G 16 20,783 332,528 AMD
8 RYZEN 9 3900XT 12-CORE 24 13,123 314,952 AMD
9 RYZEN 7 3800X 8-CORE 16 18,147 290,352 AMD
10 RYZEN 9 3900X 12-CORE 24 10,512 252,288 AMD
11 RYZEN 5 5600X 6-CORE 12 18,535 222,420 AMD
12 CORE I9-9900K CPU @ 3.60GHZ 16 13,482 215,712 Intel
13 RYZEN THREADRIPPER 2950X 16-CORE 32 6,656 212,992 AMD
14 RYZEN 9 5900HS 16 13,078 209,248 AMD
15 RYZEN 5 2600X SIX-CORE 12 15,266 183,192 AMD
16 XEON CPU E5-2690 V4 @ 2.60GHZ 28 6,474 181,272 Intel
17 CORE I7-8700 CPU @ 3.20GHZ 12 14,091 169,092 Intel
18 RYZEN 7 PRO 4750G 16 10,259 164,144 AMD
19 RYZEN 5 5600G 12 13,632 163,584 AMD
20 CORE I9-9900 CPU @ 3.10GHZ 16 10,154 162,464 Intel
21 XEON CPU E5-2680 V3 @ 2.50GHZ 24 6,658 159,792 Intel
22 RYZEN 5 3600 6-CORE 12 12,288 147,456 AMD
23 CORE I7-7700K CPU @ 4.20GHZ 8 15,523 124,184 Intel
24 11TH GEN CORE I5-11400 @ 2.60GHZ 12 9,035 108,420 Intel
25 RYZEN 5 2600 SIX-CORE 12 8,037 96,444 AMD
26 CORE I7-10750H CPU @ 2.60GHZ 12 6,996 83,952 Intel
27 CORE I7-6700K CPU @ 4.00GHZ 8 10,265 82,120 Intel
28 CORE I7-8705G CPU @ 3.10GHZ 8 9,896 79,168 Intel
29 RYZEN 5 1600 SIX-CORE 12 6,312 75,744 AMD
30 11TH GEN CORE I7-11370H @ 3.30GHZ 8 9,313 74,504 Intel
31 CORE I5-8400 CPU @ 2.80GHZ 6 12,243 73,458 Intel
32 CORE I5-8600T CPU @ 2.30GHZ 6 11,963 71,778 Intel
33 CORE I7-10510U CPU @ 1.80GHZ 8 6,947 55,576 Intel
34 CORE I5-8259U CPU @ 2.30GHZ 8 6,365 50,920 Intel
35 CORE I7-4790T CPU @ 2.70GHZ 8 6,164 49,312 Intel
36 CORE I7-3770 CPU @ 3.40GHZ 8 6,074 48,592 Intel
37 CORE I7-4770HQ CPU @ 2.20GHZ 8 5,678 45,424 Intel
38 CORE I7-4770 CPU @ 3.40GHZ 8 5,673 45,384 Intel
39 XEON CPU E3-1240 V2 @ 3.40GHZ 8 5,277 42,216 Intel
40 XEON CPU E3-1245 V2 @ 3.40GHZ 8 4,634 37,072 Intel
41 XEON CPU E31245 @ 3.30GHZ 8 4,381 35,048 Intel
42 RYZEN 7 4700U 8 4,351 34,808 AMD
43 RYZEN 5 PRO 2400G 8 4,280 34,240 AMD
44 RYZEN 5 3500U 8 3,961 31,688 AMD
45 CORE I7 CPU 975 @ 3.33GHZ 8 3,473 27,784 Intel