PROJECT #18402 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 Thursday, 30 June 2022 00:49:54

Rank
Project
Model Name
Folding@Home Identifier
Make
Brand
GPU
Model
PPD
Average
Points WU
Average
WUs Day
Average
WU Time
Average

PROJECT FOLDING PPD AVERAGES BY CPU BETA

PPDDB data as of Thursday, 30 June 2022 00:49:54

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 RYZEN 9 5900X 12-CORE 24 38,271 918,504 AMD
2 RYZEN 9 5950X 16-CORE 32 24,264 776,448 AMD
3 RYZEN 9 3950X 16-CORE 32 23,631 756,192 AMD
4 RYZEN 7 5800X 8-CORE 16 44,958 719,328 AMD
5 RYZEN 7 5700X 8-CORE 16 30,412 486,592 AMD
6 11TH GEN CORE I7-11700K @ 3.60GHZ 16 26,131 418,096 Intel
7 11TH GEN CORE I9-11900K @ 3.50GHZ 16 24,397 390,352 Intel
8 RYZEN 7 3800X 8-CORE 16 20,742 331,872 AMD
9 CORE I9-10850K CPU @ 3.60GHZ 20 15,835 316,700 Intel
10 CORE I7-10700K CPU @ 3.80GHZ 16 19,710 315,360 Intel
11 RYZEN 9 3900XT 12-CORE 24 12,482 299,568 AMD
12 12TH GEN CORE I7-12700K 20 13,895 277,900 Intel
13 CORE I9-10900X CPU @ 3.70GHZ 20 13,804 276,080 Intel
14 RYZEN 7 5800H 16 16,612 265,792 AMD
15 RYZEN 9 5900HS 16 16,416 262,656 AMD
16 EPYC 7401P 24-CORE 48 4,678 224,544 AMD
17 RYZEN 5 2600X SIX-CORE 12 17,789 213,468 AMD
18 RYZEN 5 3600 6-CORE 12 17,594 211,128 AMD
19 XEON CPU E5-2680 V3 @ 2.50GHZ 24 8,408 201,792 Intel
20 XEON CPU E5-2690 V4 @ 2.60GHZ 28 6,866 192,248 Intel
21 CORE I7-8700 CPU @ 3.20GHZ 12 14,607 175,284 Intel
22 CORE I5-9600K CPU @ 3.70GHZ 6 25,120 150,720 Intel
23 RYZEN 7 2700X EIGHT-CORE 16 9,402 150,432 AMD
24 RYZEN 7 3700X 8-CORE 16 8,946 143,136 AMD
25 11TH GEN CORE I9-11900F @ 2.50GHZ 16 7,728 123,648 Intel
26 XEON CPU E5-2650L V4 @ 1.70GHZ 28 4,313 120,764 Intel
27 CORE I7-9700K CPU @ 3.60GHZ 8 14,507 116,056 Intel
28 11TH GEN CORE I5-11400 @ 2.60GHZ 12 9,213 110,556 Intel
29 CORE I7-4790K CPU @ 4.00GHZ 8 13,001 104,008 Intel
30 RYZEN 5 1600 SIX-CORE 12 7,574 90,888 AMD
31 CORE I7-8705G CPU @ 3.10GHZ 8 9,616 76,928 Intel
32 CORE I7-4770K CPU @ 3.50GHZ 8 9,277 74,216 Intel
33 XEON CPU E5-2680 0 @ 2.70GHZ 16 4,492 71,872 Intel
34 CORE I9-8950HK CPU @ 2.90GHZ 12 5,868 70,416 Intel
35 CORE I7-6700 CPU @ 3.40GHZ 8 8,342 66,736 Intel
36 RYZEN 7 4700U 8 7,422 59,376 AMD
37 CORE I7-4770HQ CPU @ 2.20GHZ 8 7,249 57,992 Intel
38 XEON W-10855M CPU @ 2.80GHZ 12 4,657 55,884 Intel
39 CORE I5-10210U CPU @ 1.60GHZ 7 5,996 41,972 Intel
40 CORE I5-8365U CPU @ 1.60GHZ 8 4,932 39,456 Intel
41 XEON CPU E31245 @ 3.30GHZ 8 4,512 36,096 Intel
42 FX-8150 EIGHT-CORE 8 2,905 23,240 AMD
43 CORE I7 CPU 975 @ 3.33GHZ 8 2,291 18,328 Intel