Supplementary material for 'Exploring the Effect of Enhanced Sampling on Protein Stability Prediction' (doi:10.18419/darus-2132)

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Part 1: Document Description
Part 2: Study Description
Part 3: Data Files Description
Part 4: Variable Description
Part 5: Other Study-Related Materials
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Supplementary material for 'Exploring the Effect of Enhanced Sampling on Protein Stability Prediction'

doi:10.18419/darus-2132

DaRUS

2022-05-04

1

Fleck, Maximilian; Markthaler, Daniel; Stankiewicz, Bartosz; Hansen, Niels, 2022, "Supplementary material for 'Exploring the Effect of Enhanced Sampling on Protein Stability Prediction'", https://doi.org/10.18419/darus-2132, DaRUS, V1, UNF:6:8wyFNcxoOTcKA+4ZpSWLAg== [fileUNF]

Supplementary material for 'Exploring the Effect of Enhanced Sampling on Protein Stability Prediction'

doi:10.18419/darus-2132

Fleck, Maximilian (Universität Stuttgart)

Markthaler, Daniel (Universität Stuttgart)

Stankiewicz, Bartosz (Universität Stuttgart)

Hansen, Niels (Universität Stuttgart)

EXC 2075 - 390740016

DaRUS

Fleck, Maximilian

Hansen, Niels

Fleck, Maximilian

2021-09-10

https://doi.org/10.18419/darus-2132

Chemistry, Engineering, Physics, Molecular Dynamics Simulation, Protein Stability, GROMOS Force Field

Supplementary material for 'Exploring the Effect of Enhanced Sampling on Protein Stability Prediction' containing files to (re-)execute GROMACS simulations performed during the mutation study. This dataset contains simulation input files in GROMACS format accompanying the mentioned publication. Structure, topology, and simulation parameter-files are provided for the simulations discussed in the paper.<br> Due to the high number of files, the study is provided as a .zip-file. Please check the README.

Kowalski, J. A.; Liu, K.; Kelly, J. W. (2009) The NMR solution structure of the isolated Apo Pin1 WW domain. <a href="https://doi.org/10.2210/pdb2KCF/pdb">doi: 10.2210/pdb2KCF/pdb</a>

Markthaler, Daniel; Fleck, Maximilian; Stankiewicz, Bartosz; Hansen, Niels: Exploring the Effect of Enhanced Sampling on Protein Stability Prediction. Journal of Chemical Theory and Computation (2022)

10.1021/acs.jctc.1c01012

Markthaler, Daniel; Fleck, Maximilian; Stankiewicz, Bartosz; Hansen, Niels: Exploring the Effect of Enhanced Sampling on Protein Stability Prediction. Journal of Chemical Theory and Computation (2022)

• Number of cases: 9

• No. of variables per record: 8

• Type of File: text/tab-separated-values

UNF:6:xkU5nT67CY+ZuvXa5o2kkg==

• Number of cases: 44

• No. of variables per record: 9

• Type of File: text/tab-separated-values

UNF:6:8n9eAtS6YUCWloElxcJVew==

• Number of cases: 85

• No. of variables per record: 11

• Type of File: text/tab-separated-values

UNF:6:YxIlc6DpuEGTRQn+wRdRog==

• Protein - Protein
• Mutation - Mutation
• Simulation-Type - Simulation-Type
• Charge-change - Charge-change
• Temperature [KELVIN] - Temperature [KELVIN]
• Pressure [BAR] - Pressure [BAR]
• Simulation-ddG [KILOJOULE/MOL] - Simulation-ddG [KILOJOULE/MOL]
• Std-Simulation-ddG [KILOJOULE/MOL] - Std-Simulation-ddG [KILOJOULE/MOL]
• Protein - Protein
• Mutation - Mutation
• Simulation-Type - Simulation-Type
• Mutation-Path - Mutation-Path
• Fold - Fold
• Temperature [KELVIN] - Temperature [KELVIN]
• Pressure [BAR] - Pressure [BAR]
• dG [KILOJOULE/MOL] - dG [KILOJOULE/MOL]
• std [KILOJOULE/MOL] - std [KILOJOULE/MOL]
• Protein - Protein
• Mutation - Mutation
• Simulation-Type - Simulation-Type
• Charge-change - Charge-change
• Temperature - Temperature
• Pressure [BAR] - Pressure [BAR]
• Simulation-ddG [KILOJOULE/MOL] - Simulation-ddG [KILOJOULE/MOL]
• Std-Simulation-ddG [KILOJOULE/MOL] - Std-Simulation-ddG [KILOJOULE/MOL]
• Experimental-ddG [KILOJOULE/MOL] - Experimental-ddG [KILOJOULE/MOL]
• Std-Experimental-ddG [KILOJOULE/MOL] - Std-Experimental-ddG [KILOJOULE/MOL]
• Expectation - Expectation

f108325 Location:

Variable Format: character

Notes: UNF:6:yDgy3l5fJ288JdTpbX/L5w==

f108325 Location:

Variable Format: character

Notes: UNF:6:XkrePrYIic4Iu7p0VyJYhw==

f108325 Location:

Variable Format: character

Notes: UNF:6:F+3shRw5XmbxTfGE+ysSng==

f108325 Location:

Variable Format: character

Notes: UNF:6:9TBmPJzinsRi5+sQMsNj+A==

f108325 Location:

Summary Statistics: Min. 275.0; StDev 21.650635094610966; Valid 9.0; Mean 300.0; Max. 325.0

Variable Format: numeric

Notes: UNF:6:12fgsc4MoNuvHMR9YGAgUw==

f108325 Location:

Summary Statistics: Max. 1.0; StDev 0.0; Valid 9.0; Mean 1.0; Min. 1.0

Variable Format: numeric

Notes: UNF:6:BZVA++AgvYtpNee1DL+/dw==

f108325 Location:

Summary Statistics: Max. 4.044; StDev 9.61691525964075; Valid 9.0; Min. -18.37; Mean -5.202111111111111

Variable Format: numeric

Notes: UNF:6:FP2CDMNmlLg6WtMSMn+60w==

f108325 Location:

Summary Statistics: Mean 0.2778888888888889; Max. 0.98; Min. 0.014; Valid 9.0; StDev 0.3150041445935452

Variable Format: numeric

Notes: UNF:6:HLK7GMok/RJfTsSj9EnFLg==

f108327 Location:

Variable Format: character

Notes: UNF:6:f3uvcTkLA0jINbCqX0EOhg==

f108327 Location:

Variable Format: character

Notes: UNF:6:d3AkYvZaA9LM4CbAa3ruxg==

f108327 Location:

Variable Format: character

Notes: UNF:6:LYkyaRCsIFucwbEKD3sxHQ==

f108327 Location:

Summary Statistics: Min. 1.0; Mean 89.5; StDev 113.8402593600471; Valid 44.0; Max. 321.0;

Variable Format: numeric

Notes: UNF:6:z/OQaIGpxgXdthYdFP/BhQ==

f108327 Location:

Variable Format: character

Notes: UNF:6:vQzQTtaC90+77JLjJsmlrw==

f108327 Location:

Summary Statistics: StDev 0.0; Valid 44.0; Min. 298.0; Max. 298.0; Mean 298.0

Variable Format: numeric

Notes: UNF:6:wGBeVkvE1DPfxnUy01qn5Q==

f108327 Location:

Summary Statistics: Mean 1.0; StDev 0.0; Valid 44.0; Min. 1.0; Max. 1.0

Variable Format: numeric

Notes: UNF:6:rNcrloIX2mecdhO5+6LyyA==

f108327 Location:

Summary Statistics: StDev 54.08549103147977; Mean -40.7925; Min. -127.8; Valid 44.0; Max. 47.88

Variable Format: numeric

Notes: UNF:6:J7NZ54LNE9RcSwbtYeFRdQ==

f108327 Location:

Summary Statistics: Mean 0.057272727272727274; Valid 44.0; Min. 0.01; Max. 0.4; StDev 0.06697322048517937;

Variable Format: numeric

Notes: UNF:6:V+pbkmG7NbeMp8yu01qLTA==

f108326 Location:

Variable Format: character

Notes: UNF:6:i5lI1bENTFArGS699+2sdg==

f108326 Location:

Variable Format: character

Notes: UNF:6:4g34onJf308+ElxYYHP2ZA==

f108326 Location:

Variable Format: character

Notes: UNF:6:WBgjShA6HrtIq5/xYk8c0w==

f108326 Location:

Variable Format: character

Notes: UNF:6:GDMeGjsFYLe6gCykQTxVPg==

f108326 Location:

Summary Statistics: StDev 0.0; Mean 313.0; Valid 85.0; Max. 313.0; Min. 313.0;

Variable Format: numeric

Notes: UNF:6:fwv+PYEz1ZoMOorVGEh2zg==

f108326 Location:

Summary Statistics: StDev 0.0; Valid 85.0; Max. 1.0; Mean 1.0; Min. 1.0

Variable Format: numeric

Notes: UNF:6:iWI9VfYMUoS2s/VXC1zDrQ==

f108326 Location:

Summary Statistics: Min. -6.216; Mean 2.422541176470588; StDev 4.430548833445605; Max. 16.409; Valid 85.0

Variable Format: numeric

Notes: UNF:6:XKwMhgre6MS4y6OyX68WeA==

f108326 Location:

Summary Statistics: StDev 0.4109770444937774; Mean 0.11209058823529412; Max. 3.816; Min. 0.0057; Valid 85.0

Variable Format: numeric

Notes: UNF:6:zDGjuG5ZjDBjhiPAYYSliA==

f108326 Location:

Summary Statistics: Min. -2.2077; Mean 3.44024; Max. 13.0; StDev 3.6840508881143617; Valid 75.0;

Variable Format: numeric

Notes: UNF:6:JOiNY20Wb2hyf3oUE0JWHw==

f108326 Location:

Summary Statistics: Max. 0.6411; Min. 0.5203; Valid 55.0; StDev 0.02679303040185037; Mean 0.5662618181818182

Variable Format: numeric

Notes: UNF:6:a9qrFLEZs2GwL/CNbplXrw==

f108326 Location:

Variable Format: character

Notes: UNF:6:v8SBEoApZw1xOpJpBhk5xw==

Label:

buildHybrid.py

Text:

Python tool to prepare perturbation topologies for GROMOS

text/x-python

Label:

buildHybrid_doc.pdf

Text:

documentation of buildHybrid.py

application/pdf

Label:

DhaA-overview.xlsx

Text:

Results of the DhaA investigation. Digitalized and sorted

application/vnd.openxmlformats-officedocument.spreadsheetml.sheet

Label:

G95-overview.xlsx

Text:

Results of the G95 investigation. Digitalized and sorted

application/vnd.openxmlformats-officedocument.spreadsheetml.sheet

Label:

mutation_study.zip

Text:

Input files to reproduce the mutation studies with GROMACS

application/zip

Label:

overview-example-notebook.ipynb

Text:

Just a simple example how to use the data provided in the excel sheets

application/x-ipynb+json

Label:

PIN-WW-overview.xlsx

Text:

Results of the PIN-WW investigation. Digitalized and sorted

application/vnd.openxmlformats-officedocument.spreadsheetml.sheet

Label:

README.pdf

Text:

Readme covering contents of mutation_study.zip

application/pdf