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 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 CORE I9-8950HK CPU @ 2.90GHZ 12 211,342 2,536,104 Intel
2 RYZEN 7 5800X 8-CORE 16 47,921 766,736 AMD
3 RYZEN 9 5950X 16-CORE 32 20,433 653,856 AMD
4 RYZEN 9 3950X 16-CORE 32 15,063 482,016 AMD
5 RYZEN 7 5800X3D 8-CORE 16 28,586 457,376 AMD
6 RYZEN 7 5700X 8-CORE 16 27,435 438,960 AMD
7 12TH GEN CORE I9-12900K 24 18,233 437,592 Intel
8 12TH GEN CORE I7-12700K 20 21,130 422,600 Intel
9 RYZEN 9 5900X 12-CORE 24 16,701 400,824 AMD
10 11TH GEN CORE I9-11900K @ 3.50GHZ 16 23,426 374,816 Intel
11 11TH GEN CORE I7-11700K @ 3.60GHZ 16 21,987 351,792 Intel
12 12TH GEN CORE I5-12600K 16 19,341 309,456 Intel
13 RYZEN 9 3900XT 12-CORE 24 12,464 299,136 AMD
14 RYZEN 9 3900X 12-CORE 24 11,831 283,944 AMD
15 RYZEN 7 3800X 8-CORE 16 16,772 268,352 AMD
16 RYZEN THREADRIPPER 2970WX 24-CORE 48 5,346 256,608 AMD
17 XEON CPU E5-2690 V4 @ 2.60GHZ 28 8,396 235,088 Intel
18 CORE I9-10900X CPU @ 3.70GHZ 20 11,564 231,280 Intel
19 CORE I5-9300H CPU @ 2.40GHZ 8 25,664 205,312 Intel
20 RYZEN 9 5900HS 16 12,709 203,344 AMD
21 CORE I7-8700 CPU @ 3.20GHZ 12 16,527 198,324 Intel
22 RYZEN 5 2600X SIX-CORE 12 15,648 187,776 AMD
23 CORE I7-9700 CPU @ 3.00GHZ 8 21,722 173,776 Intel
24 RYZEN 5 5600X 6-CORE 12 14,462 173,544 AMD
25 RYZEN 7 PRO 4750G 16 10,799 172,784 AMD
26 XEON CPU E5-2698 V4 @ 2.20GHZ 16 10,395 166,320 Intel
27 CORE I5-10600 CPU @ 3.30GHZ 12 13,600 163,200 Intel
28 CORE I9-9900 CPU @ 3.10GHZ 16 10,091 161,456 Intel
29 XEON CPU E5-2680 V3 @ 2.50GHZ 24 6,498 155,952 Intel
30 RYZEN 7 4800H 16 9,698 155,168 AMD
31 RYZEN THREADRIPPER 3960X 24-CORE 48 3,130 150,240 AMD
32 12TH GEN CORE I3-12100F 8 18,692 149,536 Intel
33 RYZEN 5 5600G 12 12,104 145,248 AMD
34 RYZEN 5 3600 6-CORE 12 12,084 145,008 AMD
35 RYZEN 7 3700X 8-CORE 16 8,053 128,848 AMD
36 11TH GEN CORE I7-11850H @ 2.50GHZ 16 7,210 115,360 Intel
37 XEON CPU E5-2650 V2 @ 2.60GHZ 32 3,375 108,000 Intel
38 CORE I7-7700K CPU @ 4.20GHZ 8 12,075 96,600 Intel
39 11TH GEN CORE I5-11400 @ 2.60GHZ 12 7,969 95,628 Intel
40 APPLE M1 8 11,609 92,872 Apple
41 11TH GEN CORE I9-11900F @ 2.50GHZ 16 5,529 88,464 Intel
42 RYZEN 5 1600 SIX-CORE 12 7,123 85,476 AMD
43 CORE I5-10400 CPU @ 2.90GHZ 12 6,834 82,008 Intel
44 APPLE M1 MAX 10 8,164 81,640 Apple
45 CORE I7-6700K CPU @ 4.00GHZ 8 10,080 80,640 Intel
46 XEON CPU E5-2680 0 @ 2.70GHZ 16 4,560 72,960 Intel
47 CORE I7-4770K CPU @ 3.50GHZ 8 8,781 70,248 Intel
48 EPYC 7251 8-CORE 16 4,136 66,176 AMD
49 CORE I5-8600T CPU @ 2.30GHZ 6 10,617 63,702 Intel
50 XEON CPU E5-1630 V3 @ 3.70GHZ 8 7,806 62,448 Intel
51 CORE I7-6700 CPU @ 3.40GHZ 8 7,787 62,296 Intel
52 CORE I7-6700HQ CPU @ 2.60GHZ 8 7,648 61,184 Intel
53 RYZEN 7 2700X EIGHT-CORE 16 3,778 60,448 AMD
54 CORE I7-4790T CPU @ 2.70GHZ 8 7,243 57,944 Intel
55 XEON W-10855M CPU @ 2.80GHZ 12 4,420 53,040 Intel
56 CORE I7-4770HQ CPU @ 2.20GHZ 8 6,359 50,872 Intel
57 CORE I5-4590 CPU @ 3.30GHZ 4 12,580 50,320 Intel
58 CORE I7-3770 CPU @ 3.40GHZ 8 6,152 49,216 Intel
59 11TH GEN CORE I5-1135G7 @ 2.40GHZ 8 5,754 46,032 Intel
60 CORE I7-2600 CPU @ 3.40GHZ 8 5,339 42,712 Intel
61 CORE I5-8259U CPU @ 2.30GHZ 8 5,286 42,288 Intel
62 CORE I7-4700MQ CPU @ 2.40GHZ 8 5,117 40,936 Intel
63 XEON CPU E3-1240 V2 @ 3.40GHZ 8 4,974 39,792 Intel
64 11TH GEN CORE I7-1185G7 @ 3.00GHZ 8 4,754 38,032 Intel
65 XEON CPU E3-1245 V2 @ 3.40GHZ 8 4,188 33,504 Intel
66 XEON CPU E31245 @ 3.30GHZ 8 4,063 32,504 Intel
67 12TH GEN CORE I7-12700 20 1,560 31,200 Intel
68 XEON CPU E5-2620 0 @ 2.00GHZ 12 2,120 25,440 Intel