PROJECT #18420 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 04:36:08

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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 7 5800X 8-CORE 16 31,659 506,544 AMD
2 RYZEN 9 3950X 16-CORE 32 14,122 451,904 AMD
3 11TH GEN CORE I7-11700K @ 3.60GHZ 16 25,761 412,176 Intel
4 RYZEN 9 5950X 16-CORE 32 11,695 374,240 AMD
5 RYZEN 9 3900X 12-CORE 24 14,851 356,424 AMD
6 RYZEN 7 3800X 8-CORE 16 19,787 316,592 AMD
7 CORE I9-9900K CPU @ 3.60GHZ 16 16,652 266,432 Intel
8 RYZEN 7 2700 EIGHT-CORE 16 15,133 242,128 AMD
9 CORE I7-8700 CPU @ 3.20GHZ 12 19,944 239,328 Intel
10 RYZEN 5 2600 SIX-CORE 12 12,220 146,640 AMD
11 RYZEN 5 3600 6-CORE 12 9,028 108,336 AMD
12 11TH GEN CORE I5-11400 @ 2.60GHZ 12 9,024 108,288 Intel
13 RYZEN 7 2700X EIGHT-CORE 16 5,355 85,680 AMD