PROJECT #18403 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: 24,700

Core: GRO_A8

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

PPDDB data as of Thursday, 30 June 2022 00:49:54

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

PPDDB data as of Thursday, 30 June 2022 00:49:54

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 RYZEN 9 5900X 12-CORE 24 40,879 981,096 AMD
2 RYZEN 7 5700G 16 47,014 752,224 AMD
3 RYZEN 7 5800X 8-CORE 16 44,225 707,600 AMD
4 12TH GEN CORE I7-12700K 20 33,082 661,640 Intel
5 RYZEN 9 3950X 16-CORE 32 18,341 586,912 AMD
6 RYZEN 7 5700X 8-CORE 16 33,331 533,296 AMD
7 11TH GEN CORE I9-11900K @ 3.50GHZ 16 26,308 420,928 Intel
8 11TH GEN CORE I7-11700K @ 3.60GHZ 16 23,420 374,720 Intel
9 12TH GEN CORE I7-12700 20 17,087 341,740 Intel
10 RYZEN 9 3900X 12-CORE 24 13,585 326,040 AMD
11 RYZEN 7 3800X 8-CORE 16 20,302 324,832 AMD
12 CORE I9-7920X CPU @ 2.90GHZ 24 13,494 323,856 Intel
13 CORE I9-10850K CPU @ 3.60GHZ 20 15,712 314,240 Intel
14 RYZEN 9 5950X 16-CORE 32 9,531 304,992 AMD
15 CORE I9-10900X CPU @ 3.70GHZ 20 15,022 300,440 Intel
16 CORE I7-8700 CPU @ 3.20GHZ 12 20,494 245,928 Intel
17 RYZEN 9 5900HS 16 14,336 229,376 AMD
18 RYZEN 5 2600X SIX-CORE 12 18,132 217,584 AMD
19 RYZEN THREADRIPPER 3960X 24-CORE 48 4,513 216,624 AMD
20 XEON CPU E5-2690 V4 @ 2.60GHZ 28 7,106 198,968 Intel
21 CORE I7-10700T CPU @ 2.00GHZ 16 12,354 197,664 Intel
22 RYZEN 5 3600 6-CORE 12 15,615 187,380 AMD
23 RYZEN 7 PRO 4750G 16 11,502 184,032 AMD
24 RYZEN 5 5600X 6-CORE 12 13,603 163,236 AMD
25 CORE I5-10400 CPU @ 2.90GHZ 12 12,391 148,692 Intel
26 XEON CPU E5-2698 V4 @ 2.20GHZ 16 9,172 146,752 Intel
27 RYZEN 7 3700X 8-CORE 16 8,530 136,480 AMD
28 11TH GEN CORE I5-11400 @ 2.60GHZ 12 9,265 111,180 Intel
29 CORE I7-5820K CPU @ 3.30GHZ 12 8,686 104,232 Intel
30 RYZEN 5 1600 SIX-CORE 12 8,158 97,896 AMD
31 RYZEN 5 2600 SIX-CORE 12 7,243 86,916 AMD
32 CORE I7-4790K CPU @ 4.00GHZ 8 10,619 84,952 Intel
33 CORE I7-6700K CPU @ 4.00GHZ 8 10,048 80,384 Intel
34 CORE I9-8950HK CPU @ 2.90GHZ 12 6,394 76,728 Intel
35 CORE I5-8600T CPU @ 2.30GHZ 6 12,541 75,246 Intel
36 CORE I7-8705G CPU @ 3.10GHZ 8 9,297 74,376 Intel
37 11TH GEN CORE I7-1185G7 @ 3.00GHZ 8 9,229 73,832 Intel
38 CORE I7-4770 CPU @ 3.40GHZ 8 8,560 68,480 Intel
39 CORE I5-10500T CPU @ 2.30GHZ 12 5,685 68,220 Intel
40 CORE I7-4770HQ CPU @ 2.20GHZ 8 6,862 54,896 Intel
41 11TH GEN CORE I5-1135G7 @ 2.40GHZ 8 6,829 54,632 Intel
42 XEON CPU E3-1270 V2 @ 3.50GHZ 8 6,553 52,424 Intel
43 RYZEN 5 3500 6-CORE 6 8,214 49,284 AMD
44 CORE I5-8259U CPU @ 2.30GHZ 8 4,809 38,472 Intel
45 XEON CPU E3-1245 V2 @ 3.40GHZ 8 3,946 31,568 Intel
46 XEON CPU E31245 @ 3.30GHZ 8 3,873 30,984 Intel
47 11TH GEN CORE I5-1155G7 @ 2.50GHZ 8 3,322 26,576 Intel