PROJECT #18418 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 Monday, 03 October 2022 12:16:28

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 Monday, 03 October 2022 12:16:28

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 RYZEN 7 5800X 8-CORE 16 42,094 673,504 AMD
2 RYZEN 7 5800X3D 8-CORE 16 27,448 439,168 AMD
3 12TH GEN CORE I9-12900K 24 18,220 437,280 Intel
4 12TH GEN CORE I7-12700K 20 20,928 418,560 Intel
5 RYZEN 9 3900 12-CORE 24 16,776 402,624 AMD
6 RYZEN 9 3950X 16-CORE 32 11,837 378,784 AMD
7 11TH GEN CORE I9-11900K @ 3.50GHZ 16 23,404 374,464 Intel
8 11TH GEN CORE I7-11700K @ 3.60GHZ 16 20,751 332,016 Intel
9 RYZEN 7 5800H 16 18,226 291,616 AMD
10 RYZEN 7 3800X 8-CORE 16 18,153 290,448 AMD
11 CORE I9-10850K CPU @ 3.60GHZ 20 13,033 260,660 Intel
12 XEON CPU E5-2690 V4 @ 2.60GHZ 28 8,788 246,064 Intel
13 RYZEN 5 3600X 6-CORE 12 20,373 244,476 AMD
14 CORE I9-7920X CPU @ 2.90GHZ 24 10,132 243,168 Intel
15 RYZEN 5 5600G 12 20,187 242,244 AMD
16 RYZEN 5 5600X 6-CORE 12 20,176 242,112 AMD
17 RYZEN 7 5700G 16 14,815 237,040 AMD
18 RYZEN 9 5950X 16-CORE 32 7,069 226,208 AMD
19 RYZEN 9 5900HS 16 13,521 216,336 AMD
20 RYZEN 9 3900XT 12-CORE 24 8,644 207,456 AMD
21 CORE I7-8700 CPU @ 3.20GHZ 12 16,919 203,028 Intel
22 CORE I9-9900K CPU @ 3.60GHZ 16 12,312 196,992 Intel
23 RYZEN 5 2600X SIX-CORE 12 15,959 191,508 AMD
24 CORE I9-10900X CPU @ 3.70GHZ 20 9,545 190,900 Intel
25 CORE I7-4790K CPU @ 4.00GHZ 8 22,419 179,352 Intel
26 RYZEN 9 3900X 12-CORE 24 7,344 176,256 AMD
27 CORE I7-5960X CPU @ 3.00GHZ 16 10,965 175,440 Intel
28 CORE I7-9700 CPU @ 3.00GHZ 8 21,848 174,784 Intel
29 RYZEN 7 4800H 16 10,541 168,656 AMD
30 XEON CPU E5-2698 V4 @ 2.20GHZ 16 10,336 165,376 Intel
31 RYZEN 7 PRO 4750G 16 9,880 158,080 AMD
32 CORE I7-9700K CPU @ 3.60GHZ 8 18,731 149,848 Intel
33 APPLE M1 MAX 10 14,557 145,570 Apple
34 RYZEN 5 3600 6-CORE 12 11,611 139,332 AMD
35 RYZEN 7 2700X EIGHT-CORE 16 7,989 127,824 AMD
36 11TH GEN CORE I9-11900F @ 2.50GHZ 16 7,277 116,432 Intel
37 11TH GEN CORE I5-11400 @ 2.60GHZ 12 9,153 109,836 Intel
38 CORE I7-10700T CPU @ 2.00GHZ 16 6,000 96,000 Intel
39 RYZEN 5 1600 SIX-CORE 12 7,224 86,688 AMD
40 RYZEN 5 2600 SIX-CORE 12 6,785 81,420 AMD
41 CORE I9-8950HK CPU @ 2.90GHZ 12 6,711 80,532 Intel
42 CORE I7-10750H CPU @ 2.60GHZ 12 6,564 78,768 Intel
43 CORE I7-8705G CPU @ 3.10GHZ 8 9,559 76,472 Intel
44 RYZEN 7 3700X 8-CORE 16 4,651 74,416 AMD
45 APPLE M1 8 8,730 69,840 Apple
46 CORE I7-4790 CPU @ 3.60GHZ 8 8,053 64,424 Intel
47 XEON CPU E5-1630 V3 @ 3.70GHZ 8 7,958 63,664 Intel
48 CORE I7-6700 CPU @ 3.40GHZ 8 7,684 61,472 Intel
49 CORE I5-8600T CPU @ 2.30GHZ 6 10,077 60,462 Intel
50 CORE I7-6700HQ CPU @ 2.60GHZ 8 7,527 60,216 Intel
51 RYZEN 5 3500 6-CORE 6 9,975 59,850 AMD
52 APPLE M1 PRO 10 4,926 49,260 Apple
53 CORE I7-4790T CPU @ 2.70GHZ 8 6,151 49,208 Intel
54 CORE I5-1035G4 CPU @ 1.10GHZ 8 6,096 48,768 Intel
55 CORE I7-3770 CPU @ 3.40GHZ 8 5,994 47,952 Intel
56 CORE I5-4590 CPU @ 3.30GHZ 4 11,920 47,680 Intel
57 CORE I7-4770HQ CPU @ 2.20GHZ 8 5,842 46,736 Intel
58 XEON CPU E5-2697 V2 @ 2.70GHZ 24 1,928 46,272 Intel
59 CORE I3-10100 CPU @ 3.60GHZ 8 5,481 43,848 Intel
60 CORE I7-4770K CPU @ 3.50GHZ 8 5,418 43,344 Intel
61 XEON CPU E3-1240 V2 @ 3.40GHZ 8 5,359 42,872 Intel
62 CORE I5-8250U CPU @ 1.60GHZ 8 5,004 40,032 Intel
63 CORE I5-8259U CPU @ 2.30GHZ 8 4,473 35,784 Intel
64 XEON CPU E3-1245 V2 @ 3.40GHZ 8 4,177 33,416 Intel
65 XEON CPU E31245 @ 3.30GHZ 8 3,666 29,328 Intel
66 CORE I7-2760QM CPU @ 2.40GHZ 8 2,896 23,168 Intel
67 OPTERON(TM) 6380 64 334 21,376 AMD