PROJECT #18408 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 3950X 16-CORE 32 22,369 715,808 AMD
2 RYZEN 9 5950X 16-CORE 32 18,308 585,856 AMD
3 RYZEN 7 5700G 16 29,144 466,304 AMD
4 CORE I9-10850K CPU @ 3.60GHZ 20 16,159 323,180 Intel
5 RYZEN 9 3900X 12-CORE 24 12,217 293,208 AMD
6 RYZEN THREADRIPPER 2950X 16-CORE 32 8,622 275,904 AMD
7 CORE I9-9900K CPU @ 3.60GHZ 16 14,810 236,960 Intel
8 XEON CPU E5-2680 V3 @ 2.50GHZ 24 9,039 216,936 Intel
9 11TH GEN CORE I9-11900K @ 3.50GHZ 16 12,624 201,984 Intel
10 RYZEN 7 2700X EIGHT-CORE 16 4,201 67,216 AMD
11 OPTERON(TM) 6380 64 330 21,120 AMD