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.

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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 Monday, 23 May 2022 03:34:39

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 Monday, 23 May 2022 03:34:39

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 45,606 729,696 AMD
2 RYZEN 9 5950X 16-CORE 32 13,558 433,856 AMD
3 RYZEN 9 3950X 16-CORE 32 11,837 378,784 AMD
4 11TH GEN CORE I9-11900K @ 3.50GHZ 16 23,404 374,464 Intel
5 RYZEN 7 3700X 8-CORE 16 22,557 360,912 AMD
6 11TH GEN CORE I7-11700K @ 3.60GHZ 16 20,445 327,120 Intel
7 RYZEN 7 3800X 8-CORE 16 18,320 293,120 AMD
8 CORE I9-10850K CPU @ 3.60GHZ 20 13,033 260,660 Intel
9 XEON CPU E5-2690 V4 @ 2.60GHZ 28 8,788 246,064 Intel
10 RYZEN 5 3600X 6-CORE 12 20,373 244,476 AMD
11 CORE I9-7920X CPU @ 2.90GHZ 24 10,132 243,168 Intel
12 RYZEN 5 5600X 6-CORE 12 20,176 242,112 AMD
13 RYZEN 9 5900HS 16 13,521 216,336 AMD
14 RYZEN 9 3900XT 12-CORE 24 8,644 207,456 AMD
15 CORE I9-9900K CPU @ 3.60GHZ 16 12,312 196,992 Intel
16 CORE I7-8700 CPU @ 3.20GHZ 12 16,405 196,860 Intel
17 RYZEN 5 2600X SIX-CORE 12 15,959 191,508 AMD
18 CORE I9-10900X CPU @ 3.70GHZ 20 9,545 190,900 Intel
19 CORE I7-4790K CPU @ 4.00GHZ 8 22,419 179,352 Intel
20 RYZEN 9 3900X 12-CORE 24 7,344 176,256 AMD
21 CORE I7-5960X CPU @ 3.00GHZ 16 10,965 175,440 Intel
22 CORE I7-9700 CPU @ 3.00GHZ 8 21,848 174,784 Intel
23 RYZEN 7 4800H 16 10,541 168,656 AMD
24 CORE I7-9700K CPU @ 3.60GHZ 8 20,106 160,848 Intel
25 RYZEN 7 PRO 4750G 16 8,938 143,008 AMD
26 RYZEN 5 3600 6-CORE 12 11,093 133,116 AMD
27 11TH GEN CORE I9-11900F @ 2.50GHZ 16 7,277 116,432 Intel
28 11TH GEN CORE I5-11400 @ 2.60GHZ 12 9,153 109,836 Intel
29 RYZEN 5 1600 SIX-CORE 12 7,224 86,688 AMD
30 CORE I9-8950HK CPU @ 2.90GHZ 12 6,899 82,788 Intel
31 RYZEN 5 2600 SIX-CORE 12 6,785 81,420 AMD
32 CORE I7-10750H CPU @ 2.60GHZ 12 6,564 78,768 Intel
33 CORE I7-8705G CPU @ 3.10GHZ 8 9,559 76,472 Intel
34 CORE I7-4790 CPU @ 3.60GHZ 8 8,053 64,424 Intel
35 XEON CPU E5-1630 V3 @ 3.70GHZ 8 7,958 63,664 Intel
36 CORE I7-6700 CPU @ 3.40GHZ 8 7,684 61,472 Intel
37 CORE I5-8600T CPU @ 2.30GHZ 6 10,077 60,462 Intel
38 CORE I7-6700HQ CPU @ 2.60GHZ 8 7,527 60,216 Intel
39 RYZEN 5 3500 6-CORE 6 9,975 59,850 AMD
40 CORE I7-4790T CPU @ 2.70GHZ 8 6,151 49,208 Intel
41 CORE I5-1035G4 CPU @ 1.10GHZ 8 6,096 48,768 Intel
42 CORE I7-3770 CPU @ 3.40GHZ 8 6,022 48,176 Intel
43 CORE I5-4590 CPU @ 3.30GHZ 4 11,920 47,680 Intel
44 CORE I7-4770HQ CPU @ 2.20GHZ 8 5,808 46,464 Intel
45 XEON CPU E5-2697 V2 @ 2.70GHZ 24 1,928 46,272 Intel
46 CORE I3-10100 CPU @ 3.60GHZ 8 5,481 43,848 Intel
47 CORE I7-4770K CPU @ 3.50GHZ 8 5,418 43,344 Intel
48 XEON CPU E3-1240 V2 @ 3.40GHZ 8 5,359 42,872 Intel
49 CORE I5-8259U CPU @ 2.30GHZ 8 4,473 35,784 Intel
50 XEON CPU E3-1245 V2 @ 3.40GHZ 8 4,177 33,416 Intel
51 XEON CPU E31245 @ 3.30GHZ 8 3,666 29,328 Intel
52 OPTERON(TM) 6380 64 334 21,376 AMD