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: 0xa8

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

PPDDB data as of Thursday, 01 December 2022 06:13:24

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, 01 December 2022 06:13:24

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 RYZEN 9 7950X 16-CORE 32 25,621 819,872 AMD
2 RYZEN 9 3950X 16-CORE 32 23,631 756,192 AMD
3 RYZEN 7 5800X 8-CORE 16 45,077 721,232 AMD
4 RYZEN 7 7700X 8-CORE 16 43,084 689,344 AMD
5 RYZEN 7 5800X3D 8-CORE 16 42,947 687,152 AMD
6 RYZEN 9 5950X 16-CORE 32 21,158 677,056 AMD
7 RYZEN 9 5900X 12-CORE 24 27,735 665,640 AMD
8 RYZEN 7 5700G 16 39,320 629,120 AMD
9 RYZEN 7 5700X 8-CORE 16 25,778 412,448 AMD
10 11TH GEN CORE I9-11900K @ 3.50GHZ 16 24,397 390,352 Intel
11 12TH GEN CORE I7-12700K 20 16,097 321,940 Intel
12 RYZEN 7 3800X 8-CORE 16 20,053 320,848 AMD
13 11TH GEN CORE I7-11700K @ 3.60GHZ 16 19,994 319,904 Intel
14 CORE I7-10700K CPU @ 3.80GHZ 16 19,710 315,360 Intel
15 RYZEN 5 5600X 6-CORE 12 25,190 302,280 AMD
16 RYZEN 9 3900XT 12-CORE 24 12,482 299,568 AMD
17 CORE I9-10900X CPU @ 3.70GHZ 20 14,715 294,300 Intel
18 RYZEN 5 5600G 12 24,493 293,916 AMD
19 CORE I9-10850K CPU @ 3.60GHZ 20 14,459 289,180 Intel
20 RYZEN 9 3900X 12-CORE 24 11,194 268,656 AMD
21 RYZEN 9 5900HS 16 16,416 262,656 AMD
22 RYZEN 7 5800H 16 14,252 228,032 AMD
23 EPYC 7401P 24-CORE 48 4,678 224,544 AMD
24 XEON CPU E5-2680 V3 @ 2.50GHZ 24 8,408 201,792 Intel
25 XEON CPU E5-2690 V4 @ 2.60GHZ 28 6,866 192,248 Intel
26 RYZEN 5 3600 6-CORE 12 15,936 191,232 AMD
27 RYZEN 5 2600X SIX-CORE 12 15,425 185,100 AMD
28 CORE I7-10750H CPU @ 2.60GHZ 12 15,151 181,812 Intel
29 XEON CPU E5-2650L V4 @ 1.70GHZ 28 5,966 167,048 Intel
30 RYZEN 7 PRO 4750G 16 10,398 166,368 AMD
31 CORE I7-8700 CPU @ 3.20GHZ 12 13,809 165,708 Intel
32 RYZEN 7 3700X 8-CORE 16 10,344 165,504 AMD
33 12TH GEN CORE I3-12100 8 19,146 153,168 Intel
34 CORE I5-9600K CPU @ 3.70GHZ 6 25,120 150,720 Intel
35 RYZEN 7 2700X EIGHT-CORE 16 9,402 150,432 AMD
36 XEON GOLD 6128 CPU @ 3.40GHZ 12 12,411 148,932 Intel
37 XEON CPU E5-2650 V2 @ 2.60GHZ 32 4,347 139,104 Intel
38 CORE I7-9700K CPU @ 3.60GHZ 8 17,364 138,912 Intel
39 11TH GEN CORE I9-11900F @ 2.50GHZ 16 7,728 123,648 Intel
40 11TH GEN CORE I5-11400 @ 2.60GHZ 12 9,594 115,128 Intel
41 CORE I7-4790K CPU @ 4.00GHZ 8 13,001 104,008 Intel
42 XEON CPU E3-1270 V5 @ 3.60GHZ 8 11,088 88,704 Intel
43 RYZEN 5 1600 SIX-CORE 12 7,014 84,168 AMD
44 CORE I9-8950HK CPU @ 2.90GHZ 12 6,755 81,060 Intel
45 APPLE M1 MAX 10 8,039 80,390 Apple
46 CORE I7-8705G CPU @ 3.10GHZ 8 9,616 76,928 Intel
47 APPLE M1 8 8,533 68,264 Apple
48 CORE I7-6700 CPU @ 3.40GHZ 8 8,342 66,736 Intel
49 XEON CPU E5-2680 0 @ 2.70GHZ 16 4,014 64,224 Intel
50 RYZEN 7 4700U 8 7,422 59,376 AMD
51 CORE I7-4770HQ CPU @ 2.20GHZ 8 7,374 58,992 Intel
52 XEON W-10855M CPU @ 2.80GHZ 12 4,657 55,884 Intel
53 CORE I7-4770K CPU @ 3.50GHZ 8 5,986 47,888 Intel
54 CORE I5-10210U CPU @ 1.60GHZ 7 5,996 41,972 Intel
55 CORE I5-8365U CPU @ 1.60GHZ 8 4,932 39,456 Intel
56 XEON CPU E31245 @ 3.30GHZ 8 4,512 36,096 Intel
57 CORE I7-2760QM CPU @ 2.40GHZ 8 3,225 25,800 Intel
58 FX-8150 EIGHT-CORE 8 2,905 23,240 AMD
59 CORE I7 CPU 975 @ 3.33GHZ 8 2,291 18,328 Intel