PROJECT #18409 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 CORE I9-10850K CPU @ 3.60GHZ 20 36,403 728,060 Intel
2 RYZEN 9 3950X 16-CORE 32 16,069 514,208 AMD
3 11TH GEN CORE I7-11700K @ 3.60GHZ 16 25,374 405,984 Intel
4 RYZEN 9 3900X 12-CORE 24 12,309 295,416 AMD
5 RYZEN 9 5950X 16-CORE 32 9,189 294,048 AMD
6 CORE I9-10900X CPU @ 3.70GHZ 20 13,481 269,620 Intel
7 CORE I9-9900X CPU @ 3.50GHZ 20 12,095 241,900 Intel
8 CORE I9-9900 CPU @ 3.10GHZ 16 14,721 235,536 Intel
9 11TH GEN CORE I9-11900K @ 3.50GHZ 16 13,799 220,784 Intel
10 RYZEN 9 3900XT 12-CORE 24 8,491 203,784 AMD
11 11TH GEN CORE I7-11850H @ 2.50GHZ 16 12,543 200,688 Intel
12 11TH GEN CORE I9-11900F @ 2.50GHZ 16 10,385 166,160 Intel
13 CORE I7-10870H CPU @ 2.20GHZ 16 8,399 134,384 Intel
14 CORE I9-9880H CPU @ 2.30GHZ 16 7,288 116,608 Intel