PROJECT #18405 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 35,661 1,141,152 AMD
2 RYZEN 7 5800X 8-CORE 16 34,992 559,872 AMD
3 RYZEN 9 5950X 16-CORE 32 13,600 435,200 AMD
4 RYZEN 7 3800X 8-CORE 16 21,425 342,800 AMD
5 CORE I9-10850K CPU @ 3.60GHZ 20 16,758 335,160 Intel
6 CORE I9-9900K CPU @ 3.60GHZ 16 18,239 291,824 Intel
7 CORE I7-8700 CPU @ 3.20GHZ 12 20,489 245,868 Intel
8 XEON CPU E5-2680 V3 @ 2.50GHZ 24 10,089 242,136 Intel
9 RYZEN THREADRIPPER 3960X 24-CORE 48 4,542 218,016 AMD
10 RYZEN 5 2600X SIX-CORE 12 17,448 209,376 AMD
11 CORE I7-6700K CPU @ 4.00GHZ 8 9,344 74,752 Intel
12 11TH GEN CORE I7-1165G7 @ 2.80GHZ 8 1,169 9,352 Intel