PROJECT #18410 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: 64,500

Core: GRO_A8

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

PPDDB data as of Friday, 03 December 2021 04:36:08

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PROJECT FOLDING PPD AVERAGES BY CPU BETA

PPDDB data as of Friday, 03 December 2021 04:36:08

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 27,460 878,720 AMD
2 RYZEN 9 3950X 16-CORE 32 19,573 626,336 AMD
3 RYZEN 7 5800X 8-CORE 16 31,222 499,552 AMD
4 RYZEN 9 3900X 12-CORE 24 18,722 449,328 AMD
5 RYZEN THREADRIPPER 2950X 16-CORE 32 13,322 426,304 AMD
6 CORE I9-10850K CPU @ 3.60GHZ 20 16,348 326,960 Intel
7 RYZEN 7 3800X 8-CORE 16 19,190 307,040 AMD
8 RYZEN 9 5900X 12-CORE 24 12,068 289,632 AMD
9 CORE I7-10870H CPU @ 2.20GHZ 16 17,541 280,656 Intel
10 CORE I9-10900X CPU @ 3.70GHZ 20 13,590 271,800 Intel
11 XEON CPU E5-2680 V3 @ 2.50GHZ 24 11,282 270,768 Intel
12 CORE I9-9900K CPU @ 3.60GHZ 16 15,946 255,136 Intel
13 CORE I7-10700 CPU @ 2.90GHZ 16 10,193 163,088 Intel
14 11TH GEN CORE I9-11900F @ 2.50GHZ 16 8,739 139,824 Intel