PROJECT #18406 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.

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 Sunday, 16 January 2022 11:42:01

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PROJECT FOLDING PPD AVERAGES BY CPU BETA

PPDDB data as of Sunday, 16 January 2022 11:42:01

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 RYZEN 9 3950X 16-CORE 32 28,018 896,576 AMD
2 RYZEN 7 5800X 8-CORE 16 49,939 799,024 AMD
3 RYZEN 9 5950X 16-CORE 32 23,298 745,536 AMD
4 CORE I9-10850K CPU @ 3.60GHZ 20 17,413 348,260 Intel
5 RYZEN 7 3800X 8-CORE 16 20,924 334,784 AMD
6 RYZEN 5 5600X 6-CORE 12 21,914 262,968 AMD
7 CORE I7-8700 CPU @ 3.20GHZ 12 20,543 246,516 Intel
8 RYZEN 5 2600X SIX-CORE 12 18,315 219,780 AMD
9 RYZEN 7 PRO 4750G 16 12,206 195,296 AMD
10 CORE I9-9900 CPU @ 3.10GHZ 16 12,117 193,872 Intel
11 XEON CPU E5-2690 V4 @ 2.60GHZ 28 6,817 190,876 Intel
12 RYZEN 7 1700 EIGHT-CORE 16 11,717 187,472 AMD
13 XEON CPU E5-2680 V3 @ 2.50GHZ 24 7,786 186,864 Intel
14 RYZEN 5 3600 6-CORE 12 15,535 186,420 AMD
15 RYZEN THREADRIPPER 3960X 24-CORE 48 3,623 173,904 AMD
16 CORE I7-5820K CPU @ 3.30GHZ 12 10,030 120,360 Intel
17 RYZEN 5 1600 SIX-CORE 12 7,121 85,452 AMD
18 CORE I5-8400 CPU @ 2.80GHZ 6 13,235 79,410 Intel
19 CORE I7-4770HQ CPU @ 2.20GHZ 8 7,342 58,736 Intel
20 CORE I9-8950HK CPU @ 2.90GHZ 12 4,576 54,912 Intel
21 XEON CPU E31245 @ 3.30GHZ 8 4,905 39,240 Intel
22 XEON CPU E5-2620 0 @ 2.00GHZ 12 2,577 30,924 Intel
23 11TH GEN CORE I5-1135G7 @ 2.40GHZ 8 3,608 28,864 Intel