PROJECT #18412 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: 64,500

Core: 0xa8

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

PPDDB data as of Friday, 03 February 2023 06:15:11

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 Friday, 03 February 2023 06:15:11

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 20,295 649,440 AMD
2 RYZEN 7 7700X 8-CORE 16 39,395 630,320 AMD
3 RYZEN 7 5800X3D 8-CORE 16 38,003 608,048 AMD
4 12TH GEN CORE I9-12900K 24 24,333 583,992 Intel
5 12TH GEN CORE I7-12700K 20 25,489 509,780 Intel
6 RYZEN 9 3950X 16-CORE 32 15,438 494,016 AMD
7 RYZEN 7 5800X 8-CORE 16 29,438 471,008 AMD
8 RYZEN 9 5900X 12-CORE 24 18,865 452,760 AMD
9 RYZEN 7 5700G 16 28,273 452,368 AMD
10 12TH GEN CORE I7-12700 20 21,936 438,720 Intel
11 RYZEN 7 5700X 8-CORE 16 26,761 428,176 AMD
12 RYZEN 9 3900 12-CORE 24 17,283 414,792 AMD
13 RYZEN 9 3900XT 12-CORE 24 14,067 337,608 AMD
14 RYZEN 7 3800X 8-CORE 16 20,012 320,192 AMD
15 CORE I9-10850K CPU @ 3.60GHZ 20 15,447 308,940 Intel
16 RYZEN 9 5900 12-CORE 24 12,322 295,728 AMD
17 XEON CPU E5-2680 V2 @ 2.80GHZ 40 7,097 283,880 Intel
18 RYZEN 9 3900X 12-CORE 24 9,214 221,136 AMD
19 XEON CPU E5-2680 V3 @ 2.50GHZ 24 9,107 218,568 Intel
20 CORE I9-7920X CPU @ 2.90GHZ 24 9,058 217,392 Intel
21 11TH GEN CORE I7-11700K @ 3.60GHZ 16 13,564 217,024 Intel
22 XEON CPU E5-2650 V2 @ 2.60GHZ 32 6,773 216,736 Intel
23 XEON CPU E5-2660 V3 @ 2.60GHZ 20 10,566 211,320 Intel
24 RYZEN 7 3700X 8-CORE 16 12,979 207,664 AMD
25 CORE I9-9900K CPU @ 3.60GHZ 16 12,948 207,168 Intel
26 CORE I9-10900X CPU @ 3.70GHZ 20 10,271 205,420 Intel
27 RYZEN 7 PRO 4750G 16 12,608 201,728 AMD
28 CORE I9-9900 CPU @ 3.10GHZ 16 12,228 195,648 Intel
29 CORE I7-10700K CPU @ 3.80GHZ 16 11,947 191,152 Intel
30 11TH GEN CORE I7-11850H @ 2.50GHZ 16 11,476 183,616 Intel
31 12TH GEN CORE I9-12900H 20 8,446 168,920 Intel
32 RYZEN 9 5900HX 16 9,998 159,968 AMD
33 RYZEN 7 2700X EIGHT-CORE 16 9,879 158,064 AMD
34 CORE I7-10700 CPU @ 2.90GHZ 16 7,632 122,112 Intel
35 XEON CPU E5-2690 V2 @ 3.00GHZ 20 6,017 120,340 Intel
36 CORE I7-10700T CPU @ 2.00GHZ 16 7,090 113,440 Intel
37 RYZEN 7 1800X EIGHT-CORE 16 7,040 112,640 AMD
38 XEON CPU E5-2670 0 @ 2.60GHZ 32 3,106 99,392 Intel
39 XEON CPU E5-2680 0 @ 2.70GHZ 16 5,273 84,368 Intel
40 XEON CPU E5-2697 V2 @ 2.70GHZ 24 3,314 79,536 Intel
41 XEON CPU E5-2450 0 @ 2.10GHZ 10 6,157 61,570 Intel
42 XEON CPU E5-2620 V3 @ 2.40GHZ 12 4,252 51,024 Intel