PROJECT #18425 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: 80,500

Core: GRO_A8

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

PPDDB data as of Friday, 03 December 2021 04:36:07

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PROJECT FOLDING PPD AVERAGES BY CPU BETA

PPDDB data as of Friday, 03 December 2021 04:36:07

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 RYZEN 9 5950X 16-CORE 32 38,725 1,239,200 AMD
2 RYZEN 9 3950X 16-CORE 32 23,368 747,776 AMD
3 RYZEN 9 3900X 12-CORE 24 19,571 469,704 AMD
4 RYZEN THREADRIPPER 2970WX 24-CORE 48 9,253 444,144 AMD
5 RYZEN 7 3800X 8-CORE 16 20,186 322,976 AMD
6 XEON CPU E5-2690 V4 @ 2.60GHZ 28 11,443 320,404 Intel
7 CORE I9-10850K CPU @ 3.60GHZ 20 15,143 302,860 Intel
8 RYZEN THREADRIPPER 2950X 16-CORE 32 9,243 295,776 AMD
9 CORE I9-9900K CPU @ 3.60GHZ 16 17,397 278,352 Intel
10 CORE I7-8700 CPU @ 3.20GHZ 12 20,149 241,788 Intel
11 CORE I9-10900X CPU @ 3.70GHZ 20 11,942 238,840 Intel
12 XEON CPU E5-2660 V3 @ 2.60GHZ 20 10,744 214,880 Intel
13 CORE I5-10400 CPU @ 2.90GHZ 12 15,477 185,724 Intel
14 RYZEN 5 3600 6-CORE 12 15,343 184,116 AMD
15 CORE I7-10750H CPU @ 2.60GHZ 12 9,929 119,148 Intel