PROJECT #18403 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 36,558 1,169,856 AMD
2 RYZEN 7 5800X 8-CORE 16 34,079 545,264 AMD
3 RYZEN 7 3800X 8-CORE 16 21,075 337,200 AMD
4 CORE I9-10850K CPU @ 3.60GHZ 20 15,712 314,240 Intel
5 CORE I9-10900X CPU @ 3.70GHZ 20 15,022 300,440 Intel
6 CORE I7-8700 CPU @ 3.20GHZ 12 20,542 246,504 Intel
7 RYZEN THREADRIPPER 3960X 24-CORE 48 4,363 209,424 AMD
8 CORE I5-10400 CPU @ 2.90GHZ 12 11,964 143,568 Intel
9 RYZEN 5 3600 6-CORE 12 9,799 117,588 AMD
10 11TH GEN CORE I5-11400 @ 2.60GHZ 12 8,860 106,320 Intel
11 CORE I7-5820K CPU @ 3.30GHZ 12 8,686 104,232 Intel
12 RYZEN 5 2600 SIX-CORE 12 7,243 86,916 AMD
13 CORE I7-6700K CPU @ 4.00GHZ 8 10,213 81,704 Intel
14 CORE I9-8950HK CPU @ 2.90GHZ 12 6,394 76,728 Intel