PROJECT #18407 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 17:59:03

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PROJECT FOLDING PPD AVERAGES BY CPU BETA

PPDDB data as of Monday, 27 September 2021 17:59:03

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 34,249 1,095,968 AMD
2 RYZEN 7 5800X 8-CORE 16 54,519 872,304 AMD
3 RYZEN 9 5950X 16-CORE 32 13,144 420,608 AMD
4 CORE I9-10850K CPU @ 3.60GHZ 20 20,782 415,640 Intel
5 RYZEN 7 3800X 8-CORE 16 22,289 356,624 AMD
6 XEON CPU E5-2680 V3 @ 2.50GHZ 24 13,394 321,456 Intel
7 CORE I7-8700 CPU @ 3.20GHZ 12 20,537 246,444 Intel
8 RYZEN 5 3600 6-CORE 12 12,075 144,900 AMD
9 RYZEN 5 2600 SIX-CORE 12 8,671 104,052 AMD
10 CORE I7-6700K CPU @ 4.00GHZ 8 9,788 78,304 Intel