PROJECT #18412 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 58,634 1,876,288 AMD
2 RYZEN 7 5700G 16 86,114 1,377,824 AMD
3 RYZEN 9 3950X 16-CORE 32 19,899 636,768 AMD
4 RYZEN 7 5800X 8-CORE 16 34,343 549,488 AMD
5 CORE I9-10850K CPU @ 3.60GHZ 20 15,447 308,940 Intel
6 RYZEN 7 3700X 8-CORE 16 16,574 265,184 AMD
7 RYZEN 9 3900X 12-CORE 24 10,470 251,280 AMD
8 CORE I9-9900K CPU @ 3.60GHZ 16 15,015 240,240 Intel
9 XEON CPU E5-2680 V3 @ 2.50GHZ 24 8,951 214,824 Intel
10 XEON CPU E5-2660 V3 @ 2.60GHZ 20 10,566 211,320 Intel
11 11TH GEN CORE I7-11700K @ 3.60GHZ 16 12,368 197,888 Intel
12 CORE I9-9900 CPU @ 3.10GHZ 16 12,228 195,648 Intel
13 11TH GEN CORE I7-11850H @ 2.50GHZ 16 11,476 183,616 Intel
14 CORE I9-10900X CPU @ 3.70GHZ 20 8,669 173,380 Intel