PROJECT #18415 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: 35,650

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 32,537 1,041,184 AMD
2 RYZEN 7 5800X 8-CORE 16 42,986 687,776 AMD
3 RYZEN 9 3950X 16-CORE 32 16,825 538,400 AMD
4 RYZEN 9 3900X 12-CORE 24 12,340 296,160 AMD
5 RYZEN THREADRIPPER 2970WX 24-CORE 48 5,346 256,608 AMD
6 RYZEN 7 3800X 8-CORE 16 15,373 245,968 AMD
7 RYZEN 5 5600X 6-CORE 12 19,173 230,076 AMD
8 CORE I9-10900X CPU @ 3.70GHZ 20 11,384 227,680 Intel
9 CORE I7-8700 CPU @ 3.20GHZ 12 17,137 205,644 Intel
10 CORE I5-9300H CPU @ 2.40GHZ 8 25,664 205,312 Intel
11 RYZEN 5 2600X SIX-CORE 12 15,648 187,776 AMD
12 RYZEN 7 3700X 8-CORE 16 10,901 174,416 AMD
13 CORE I7-9700 CPU @ 3.00GHZ 8 21,722 173,776 Intel
14 CORE I5-10600 CPU @ 3.30GHZ 12 13,600 163,200 Intel
15 CORE I9-9900 CPU @ 3.10GHZ 16 10,091 161,456 Intel
16 RYZEN THREADRIPPER 3960X 24-CORE 48 3,130 150,240 AMD
17 RYZEN 5 3600 6-CORE 12 9,465 113,580 AMD
18 CORE I7-7700K CPU @ 4.20GHZ 8 12,075 96,600 Intel
19 11TH GEN CORE I5-11400 @ 2.60GHZ 12 6,622 79,464 Intel
20 CORE I7-6700K CPU @ 4.00GHZ 8 8,892 71,136 Intel
21 EPYC 7251 8-CORE 16 4,136 66,176 AMD
22 CORE I7-6700 CPU @ 3.40GHZ 8 8,135 65,080 Intel
23 RYZEN 7 2700X EIGHT-CORE 16 3,778 60,448 AMD
24 CORE I7-4790T CPU @ 2.70GHZ 8 7,243 57,944 Intel
25 CORE I5-8259U CPU @ 2.30GHZ 8 6,857 54,856 Intel
26 XEON W-10855M CPU @ 2.80GHZ 12 4,420 53,040 Intel
27 CORE I5-4590 CPU @ 3.30GHZ 4 12,580 50,320 Intel
28 CORE I7-3770 CPU @ 3.40GHZ 8 5,971 47,768 Intel
29 CORE I7-2600 CPU @ 3.40GHZ 8 5,339 42,712 Intel