Templates for writing <scp>PyMOL</scp> scripts

Mooers, Blaine H. M.; Brown, Marina

doi:10.1002/pro.3997

Cited by 36 publications

(16 citation statements)

References 16 publications

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“…After dehydration and hydrogenation, the protein was stored in PDB format with Autodoc 1.5.6 software ( https://autodock.scripps.edu/ ). PyMol software [ 12 ] was used to analyze the important proteins in the active ingredients and target network whose degree value was greater than the average.…”

Section: Methodsmentioning

confidence: 99%

Molecular mechanism of modified Huanglian Wendan decoction in the treatment of polycystic ovary syndrome

Yang

2023

Medicine

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To investigate the mechanism of modified Huanglian Wendan decoction in the intervention of polycystic ovary syndrome (PCOS) by network pharmacology and molecular docking. The ingredients and targets of modified Huanglian Wendan decoction were retrieved from the traditional Chinese medicine Systems Pharmacology database. Related targets of PCOS were screened by Comparative Toxicogenomics Database database. Cytoscape 3.7.2 ( https://cytoscape.org/ ) was used to draw the target network diagram of “traditional Chinese medicine - ingredient - PCOS,” STRING database was used to construct the target protein interaction network. NCA tool of Cystoscape 3.7.2 was used to carried out topology analysis on PPI network, core components and key targets were obtained. Gene ontology and Kyoto encyclopedia of genes and genomes enrichment analysis were carried out for the intersection targets by David database. AutoDockTools 1.5.6 software ( https://autodock.scripps.edu/ ) was used to conduct molecular docking verification of key components and key targets. Ninety-one ingredients of the modified Huanglian Wendan decoction and 23,075 diseases targets were obtained, 155 Intersection targets of the drug and disease were obtained by R language, Veen plot was drawn. Gene ontology enrichment analysis obtained 432 biological processes, 67 cell components, 106 molecular functions. Fifty-four Kyoto encyclopedia of genes and genomes enrichment pathways ( P < .05) including tumor necrosis factor, hypoxia-induced factors-1, calcium, and drug metabolism-cytochrome P450 signaling pathway. Molecular docking showed quercetin, luteolin, kaempferol, and baicalein were stable in docking with core targets. Network pharmacology and molecular docking were used to preliminarily study the mechanism of action of modified Huanglian Wendan decoction in the treatment of PCOS, which laid foundation for future experimental research and clinical application.

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Section: Methodsmentioning

confidence: 99%

Molecular mechanism of modified Huanglian Wendan decoction in the treatment of polycystic ovary syndrome

Yang

2023

Medicine

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“…Those parts with the best binding energy were utilized for plotting. The 3D images plotted using PyMOL [ 26 ] presented the interaction between the receptor protein and the ligand.…”

Section: Methodsmentioning

confidence: 99%

Molecular Mechanism Investigation on Monomer Kaempferol of the Traditional Medicine Dingqing Tablet in Promoting Apoptosis of Acute Myeloid Leukemia HL-60 Cells

Zheng

Zhou

Liu

et al. 2022

Evidence-Based Complementary and Alternative Medicine

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The traditional medicine Dingqing Tablet produces effective efficacy in treating acute myeloid leukemia, but its specific mechanism remains to be investigated. Dingqing Tablet consists of Codonopsis, Indigo Naturalis, Cortex Moutan, Radix Notoginseng, Citrus Reticulata, and Eolite. The active components of Dingqing Tablets were screened by the TCMSP database. Meanwhile, the SwissTargetPrediction database was utilized to predict the corresponding targets. Relevant disease targets of acute myeloid leukemia were obtained from GeneCards. The obtained targets of Dingqing Tablets and genes of acute myeloid leukemia were used, and the overlapped genes were presented in the Venn diagram. A drug-component-target network was constructed via Cytoscape 3.6.0 software. Molecular docking methodology was also used with AutoDock Vina 1.1.2. Furthermore, the effects of kaempferol on the proliferation and apoptosis of HL-60 cells were identified using 3-(4,5)-dimethylthiahiazo(-z-y1)-3,5-di-phenytetrazoliumromide (MTT), 5-Ethynyl-2′-deoxyuridine (EDU), flow cytometry, and TdT-mediated dUTP nick-end labeling (TUNEL) assays. The combination of kaempferol and AKT1 was verified using an immunoprecipitation (IP) experiment and the effects of Kaempferol on HL-60 cell apoptosis by western blot (WB) and qPCR. The key component kaempferol and the core target gene AKT1 were sorted out using a drug-component target network diagram. Molecular docking results revealed that the binding energy between kaempferol and AKT1 was lower than -5 kcal/mol. MTT and EDU assays indicated that kaempferol markedly inhibited the proliferation of HL-60 cells. Flow cytometry and TUNEL assays suggested that kaempferol substantially promoted HL-60 cell apoptosis. IP assay results testified that kaempferol could bind to AKT1, thereby reducing the level of P-AKT and promoting HL-60 cell apoptosis. The monomer kaempferol of Dingqing Tablet could promote apoptosis of HL-60 cells, and the mechanism might correlate with the combination of kaempferol and AKT1, reducing the level of P-AKT and promoting the expression of the apoptotic signaling pathway.

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“…In the popular program PyMOL (10), most common functions are available via the graphical user interface (GUI). Advanced functions, however, require text commands that can be combined into elaborate analysis scripts using procedural programming (11,12). The use of molecular graphics software is a key skill set that allows structural interpretation of molecular mechanisms and formulation of new hypotheses.…”

Section: A Scientific and Pedagogical Backgroundmentioning

confidence: 99%

A Semester-Long Learning Path Teaching Computational Skills via Molecular Graphics in PyMOL

et al. 2022

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Structural biology describes biological processes at the molecular level and is an integral part of undergraduate study programs in molecular biosciences. Students are often fascinated by the visualizations created by molecular graphics software, which allow them to see the molecular world for the first time. Today, molecular visualization and structural analysis do not require expensive high-end computers but can be performed on the students' own laptops and are therefore highly suited for active learning approaches. We have designed a semester-long learning path that integrates molecular graphics and structural analysis using PyMOL into an undergraduate course in biomolecular structure and function. Compared to stand-alone PyMOL introductions, the semester-long learning path allows for an improved pedagogical design. The path progressively introduces more advanced functions in relevant scientific contexts and allows for spaced repetition. Advanced analysis functions in PyMOL are available only via the command line, so the learning path also teaches basic scripting and serves as an accessible introduction to computational thinking because a few lines of code can produce stunning results. Student surveys carried out at the end of the course suggest that the learning path supported the ability to perform structural analysis to a high degree. Moreover, a simulated exam showed that almost all students were able to carry out basic visualization tasks using PyMOL scripts, while three-quarters could undertake advanced structural analysis after following the course. In summary, integration of molecular graphics software with teaching of structural biochemistry allows a hands-on approach to analyzing molecular mechanisms and introduces biologically oriented students to computational thinking.

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Templates for writing PyMOL scripts

Cited by 36 publications

References 16 publications

Molecular mechanism of modified Huanglian Wendan decoction in the treatment of polycystic ovary syndrome

Molecular mechanism of modified Huanglian Wendan decoction in the treatment of polycystic ovary syndrome

Molecular Mechanism Investigation on Monomer Kaempferol of the Traditional Medicine Dingqing Tablet in Promoting Apoptosis of Acute Myeloid Leukemia HL-60 Cells

A Semester-Long Learning Path Teaching Computational Skills via Molecular Graphics in PyMOL

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