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 Monday, 27 September 2021 14:58:25

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PROJECT FOLDING PPD AVERAGES BY CPU BETA

PPDDB data as of Monday, 27 September 2021 14:58:25

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 34,167 1,093,344 AMD
2 RYZEN 7 5800X 8-CORE 16 54,002 864,032 AMD
3 RYZEN 9 5950X 16-CORE 32 13,961 446,752 AMD
4 RYZEN 7 3800X 8-CORE 16 20,368 325,888 AMD
5 CORE I7-8700 CPU @ 3.20GHZ 12 20,505 246,060 Intel
6 RYZEN 5 2600X SIX-CORE 12 18,315 219,780 AMD
7 XEON CPU E5-2690 V4 @ 2.60GHZ 28 6,943 194,404 Intel
8 RYZEN THREADRIPPER 3960X 24-CORE 48 3,525 169,200 AMD
9 RYZEN 5 3600 6-CORE 12 12,901 154,812 AMD
10 CORE I7-5820K CPU @ 3.30GHZ 12 10,030 120,360 Intel
11 CORE I7-4770HQ CPU @ 2.20GHZ 8 7,431 59,448 Intel
12 CORE I9-8950HK CPU @ 2.90GHZ 12 4,576 54,912 Intel