PROJECT #18414 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.

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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 Tuesday, 27 September 2022 13:39:56

Rank
Project
Model Name
Folding@Home Identifier
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Brand
GPU
Model
PPD
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PROJECT FOLDING PPD AVERAGES BY CPU BETA

PPDDB data as of Tuesday, 27 September 2022 13:39:56

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make
1 CORE I5-8365U CPU @ 1.60GHZ 8 235,865 1,886,920 Intel
2 RYZEN 7 5800X 8-CORE 16 45,968 735,488 AMD
3 RYZEN 9 5900X 12-CORE 24 24,774 594,576 AMD
4 RYZEN 7 5800X3D 8-CORE 16 29,500 472,000 AMD
5 12TH GEN CORE I7-12700K 20 23,581 471,620 Intel
6 CORE I9-9900X CPU @ 3.50GHZ 20 22,796 455,920 Intel
7 RYZEN 9 5950X 16-CORE 32 13,561 433,952 AMD
8 RYZEN 7 5700X 8-CORE 16 26,624 425,984 AMD
9 RYZEN 9 3950X 16-CORE 32 12,295 393,440 AMD
10 11TH GEN CORE I9-11900K @ 3.50GHZ 16 22,748 363,968 Intel
11 RYZEN 9 3900X 12-CORE 24 13,660 327,840 AMD
12 RYZEN 7 5700G 16 19,161 306,576 AMD
13 12TH GEN CORE I7-12700 20 15,189 303,780 Intel
14 RYZEN THREADRIPPER 2950X 16-CORE 32 9,240 295,680 AMD
15 12TH GEN CORE I5-12600K 16 17,914 286,624 Intel
16 RYZEN 7 3800X 8-CORE 16 17,602 281,632 AMD
17 CORE I7-10870H CPU @ 2.20GHZ 16 15,997 255,952 Intel
18 RYZEN 5 5600G 12 19,273 231,276 AMD
19 CORE I9-10900X CPU @ 3.70GHZ 20 11,384 227,680 Intel
20 RYZEN 5 5600X 6-CORE 12 18,640 223,680 AMD
21 XEON CPU E5-2690 V4 @ 2.60GHZ 28 7,904 221,312 Intel
22 XEON W-2175 CPU @ 2.50GHZ 28 7,761 217,308 Intel
23 CORE I9-9900K CPU @ 3.60GHZ 16 13,407 214,512 Intel
24 RYZEN 9 5900HS 16 13,346 213,536 AMD
25 RYZEN 7 5800H 16 12,141 194,256 AMD
26 RYZEN 5 2600X SIX-CORE 12 15,993 191,916 AMD
27 CORE I7-8700 CPU @ 3.20GHZ 12 15,342 184,104 Intel
28 XEON CPU E5-2698 V4 @ 2.20GHZ 16 11,407 182,512 Intel
29 CORE I7-5960X CPU @ 3.00GHZ 16 11,150 178,400 Intel
30 RYZEN 7 3700X 8-CORE 16 10,829 173,264 AMD
31 RYZEN 7 2700X EIGHT-CORE 16 10,655 170,480 AMD
32 XEON CPU E5-2680 V3 @ 2.50GHZ 24 6,681 160,344 Intel
33 RYZEN 5 3600 6-CORE 12 13,177 158,124 AMD
34 RYZEN 7 PRO 4750G 16 9,095 145,520 AMD
35 RYZEN 5 3600X 6-CORE 12 10,621 127,452 AMD
36 11TH GEN CORE I7-11800H @ 2.30GHZ 16 7,692 123,072 Intel
37 CORE I7-9700K CPU @ 3.60GHZ 8 15,376 123,008 Intel
38 XEON CPU E5-2650L V4 @ 1.70GHZ 28 4,254 119,112 Intel
39 CORE I7-9750H CPU @ 2.60GHZ 12 8,761 105,132 Intel
40 CORE I7-10700 CPU @ 2.90GHZ 16 6,459 103,344 Intel
41 CORE I7-9700KF CPU @ 3.60GHZ 8 12,351 98,808 Intel
42 CORE I7-10700T CPU @ 2.00GHZ 16 5,957 95,312 Intel
43 RYZEN 5 3600XT 6-CORE 12 7,584 91,008 AMD
44 11TH GEN CORE I5-11400 @ 2.60GHZ 12 7,330 87,960 Intel
45 RYZEN 5 1600 SIX-CORE 12 6,759 81,108 AMD
46 RYZEN 5 2600 SIX-CORE 12 6,509 78,108 AMD
47 CORE I7-8705G CPU @ 3.10GHZ 8 9,412 75,296 Intel
48 XEON W-10855M CPU @ 2.80GHZ 12 5,989 71,868 Intel
49 CORE I9-8950HK CPU @ 2.90GHZ 12 5,456 65,472 Intel
50 XEON CPU E5-2680 0 @ 2.70GHZ 16 3,938 63,008 Intel
51 CORE I3-10100 CPU @ 3.60GHZ 8 7,341 58,728 Intel
52 CORE I7-4770HQ CPU @ 2.20GHZ 8 6,413 51,304 Intel
53 CORE I7-4790T CPU @ 2.70GHZ 8 5,987 47,896 Intel
54 XEON CPU E3-1240 V2 @ 3.40GHZ 8 5,833 46,664 Intel
55 CORE I7-3770 CPU @ 3.40GHZ 8 5,795 46,360 Intel
56 CORE I7-4770 CPU @ 3.40GHZ 8 5,464 43,712 Intel
57 XEON CPU E5-1620 0 @ 3.60GHZ 8 5,081 40,648 Intel
58 CORE I5-8259U CPU @ 2.30GHZ 8 4,996 39,968 Intel
59 XEON CPU E3-1245 V2 @ 3.40GHZ 8 4,513 36,104 Intel
60 XEON CPU E31245 @ 3.30GHZ 8 3,521 28,168 Intel
61 CORE I7 CPU 975 @ 3.33GHZ 8 2,322 18,576 Intel