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Pymol molecular graphics system

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PyMOL is a molecular visualization software package for rendering and animating 3D molecular structures. It allows users to display, analyze, and manipulate molecular models, providing a powerful tool for research in fields such as biochemistry, structural biology, and drug design.

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Tools, by AutoDock (14 mentions) Maestro, by Schrödinger (8 mentions) Pymol software, by Schrödinger (7 mentions) Discovery studio, by Dassault Systèmes (4 mentions) Ucsf chimera, by Schrödinger (4 mentions) Maestro software, by Schrödinger (3 mentions) Bioluminate, by Schrödinger (3 mentions) Matplotlib, by Schrödinger (3 mentions) Prism 6, by GraphPad (3 mentions) Tools 1, by AutoDock (3 mentions) Prism 5, by GraphPad (3 mentions) Illustrator cc 2018, by Adobe (2 mentions) Molprobity, by Schrödinger (2 mentions) Cuemol, by Schrödinger (2 mentions) Gene specific primers, by Merck Group (2 mentions) Abi 3730 capillary sequencer, by Thermo Fisher Scientific (2 mentions) Bigdye terminator v3.1 cycle sequencing kit, by Thermo Fisher Scientific (2 mentions) Un scan it gel, by Silk Scientific (2 mentions) Topspin, by Bruker (2 mentions) Biovia discovery studio visualizer, by Dassault Systèmes (2 mentions)

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PyMOL Molecular Graphic System (32 citations) PyMOL Molecular (24 citations) PyMOL molecular graphic system version 1.8 (2 citations)

1 023 protocols using pymol molecular graphics system

1

Homology Modeling of PA2077 and PA2078

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PA2077 and PA2078 amino acid sequences were compared by BlastP PSI-BLAST (Position-Specific Iterated) using a BLOSUM 45 matrix with PDB database [21 (link)] in order to identify homologous proteins with available 3D structure. Template for 3D model construction was selected as that showing the highest identity score (RoxA, pdb 4b2n) compared with target proteins in multiple amino acid sequence alignments obtained by T-Coffee [26 (link)]. For alignment correction, secondary structure prediction was performed using the PSIPRED protein structure prediction server (http://bioinf.cs.ucl.ac.uk/psipred/) [34 (link)]. Alignment of conserved amino acid motifs and modeling corrections of the protein core were performed by comparison with the structure of the selected template sequence, using the visualization tool Pymol Molecular Graphics System, Version 1.5.0.4, Schrödinger, LLC (http://www.pymol.org).
A 3D homology model based on sequence alignment between proteins PA2077 and PA2078 and the template RoxA was obtained using Modeller 9.10 [35 (link)]. Both heme groups were included in the model generation but no other special restrictions were applied. The coordinate PDB files were used for structure comparison and overlapping structures were monitored using Pymol Molecular Graphics System, Version 1.5.0.4, Schrödinger, LLC.
Estupiñán M., Álvarez-García D., Barril X., Diaz P, & Manresa A. (2015). In Silico/In Vivo Insights into the Functional and Evolutionary Pathway of Pseudomonas aeruginosa Oleate-Diol Synthase. Discovery of a New Bacterial Di-Heme Cytochrome C Peroxidase Subfamily. PLoS ONE, 10(7), e0131462.
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2

Visualizing Human HMBS Protein Structure

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The 2.8-Å crystal structure of human HMBS (10 (link)) (Protein Data Bank ID: 3EQ1) was viewed in PyMOL Molecular Graphics System (v2.0; Schrödinger, LLC). Mapping of the molecular mutations and graphical representations were created on PyMOL Molecular Graphics System (v2.0; Schrödinger, LLC) (10 (link)), which involved comparing the structure of a protein simulated by the software with that of a published protein.
Yang Y., Chen X., Wu H., Peng H., Sun W., He B, & Yuan Z. (2020). A novel heterozygous mutation in the HMBS gene in a patient with acute intermittent porphyria and posterior reversible encephalopathy syndrome. Molecular Medicine Reports, 22(1), 516-524.
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3

Automated MTHFR Protein Structure Prediction

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We produced an automated full-length protein structural prediction homology modelling of MTHFR enzyme, using the protein sequence P42898 from Uniprot database, corresponding to the isoform 1 of protein. Structural predictions of MTHFR wild-type (WT) and MTHFR Leu590Arg mutant protein were carried out using I-TASSER (Iterative Threading ASSEmbly Refinement) server, including X-RAY structure of human MTHFR (6FCX PDB) as template (http://zhanglab.ccmb.med.umich.edu/I-TASSER, accessed on 19 December 2022) [35 (link)]. To overlap WT and mutant protein structures, the PDB files, obtained from I-TASSER server, were visualized with PyMOL Molecular Graphics System (The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC, New York, NY, USA) [36 (link)].
Barretta F., Uomo F., Fecarotta S., Albano L., Crisci D., Verde A., Fisco M.G., Gallo G., Dottore Stagna D., Pricolo M.R., Alagia M., Terrone G., Rossi A., Parenti G., Ruoppolo M., Mazzaccara C, & Frisso G. (2023). Contribution of Genetic Test to Early Diagnosis of Methylenetetrahydrofolate Reductase (MTHFR) Deficiency: The Experience of a Reference Center in Southern Italy. Genes, 14(5), 980.
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4

Comparative Structural Analysis of Class A β-Lactamase Enzymes

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The structure of 14 naturally mutated class A β-lactamase enzymes TEM-52 (PDB ID: 1HTZ), SHV-1 (PDB ID: 1SHV), SME-1 (PDB ID: 1DY6), NMC-A (PDB ID: 1BUE), SED-1 (PDB ID: 3BFE), CTXM-9 (PDB ID: 1YLJ), CTXM-27 (PDB ID: 1YLP), PENI (PDB ID: 3W4P), GES-2 (PDB ID: 3NI9), GES-11 (PDB ID: 3V3R), GES5 (PDB ID: 4GNU), PER-1 (PDB ID: 1E25) and PER-2 (PDB ID: 4D2O) were derived in the PDB format from RCSB-PDB database. PyMOL Molecular Graphics System, Version 2.0 Schrodinger, LLC (academic version) was used to visualize and compare enzyme structure of naturally mutated and wild-type class A β-lactamase enzymes. Furthermore, RMSD values of all the naturally mutated class A β-lactamase enzymes were calculated, as compared to wild-type TEM-1 using the PyMOL Molecular Graphics System, Version 2.0 Schrodinger, LLC (academic version). Structures of SME-1, SHV-1, and TEM-1 in complex with meropenem at 50 ns (stable state during MD simulation), were aligned to each other for comparing their structural features.
Agarwal V., Tiwari A, & Varadwaj P. (2022). Mutations responsible for the carbapenemase activity of SME-1. RSC Advances, 12(35), 22826-22842.
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5

Structural Determination of Alanine Racemase

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Molecular replacement was carried out with PHASER37 (link), using the coordinates of M. tuberculosis alanine racemase (PDB code 1XFC) with ligands and solvent molecules removed. Models were improved and refined using COOT38 (link) and PHENIX39 . A summary of the data collection and refinement statistics is given in Supplementary Table 1. The Ramachandran plot showed 97.3% and 2.7% of residues in the most favoured and in allowed regions, respectively. Figures were drawn using PyMol (The PyMol Molecular Graphics System, Version 2.0 Schrödinger, LLC).
Molecular replacement was carried out with PHASER37 (link), using the coordinates of M. tuberculosis alanine racemase (PDB code 1XFC) with ligands and solvent molecules removed. Models were improved and refined using COOT38 (link) and PHENIX39 . A summary of the data collection and refinement statistics is given in Supplementary Table 1. The Ramachandran plot showed 97.3% and 2.7% of residues in the most favoured and in allowed regions, respectively. Figures were drawn using PyMol (The PyMol Molecular Graphics System, Version 2.0 Schrödinger, LLC).
de Chiara C., Homšak M., Prosser G.A., Douglas H.L., Garza-Garcia A., Kelly G., Purkiss A.G., Tate E.W, & de Carvalho L.P. (2020). d-Cycloserine destruction by alanine racemase and the limit of irreversible inhibition. Nature chemical biology, 16(6), 686-694.
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6

Structural Determination of Alanine Racemase

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Molecular replacement was carried out with PHASER37 (link), using the coordinates of M. tuberculosis alanine racemase (PDB code 1XFC) with ligands and solvent molecules removed. Models were improved and refined using COOT38 (link) and PHENIX39 . A summary of the data collection and refinement statistics is given in Supplementary Table 1. The Ramachandran plot showed 97.3% and 2.7% of residues in the most favoured and in allowed regions, respectively. Figures were drawn using PyMol (The PyMol Molecular Graphics System, Version 2.0 Schrödinger, LLC).
Molecular replacement was carried out with PHASER37 (link), using the coordinates of M. tuberculosis alanine racemase (PDB code 1XFC) with ligands and solvent molecules removed. Models were improved and refined using COOT38 (link) and PHENIX39 . A summary of the data collection and refinement statistics is given in Supplementary Table 1. The Ramachandran plot showed 97.3% and 2.7% of residues in the most favoured and in allowed regions, respectively. Figures were drawn using PyMol (The PyMol Molecular Graphics System, Version 2.0 Schrödinger, LLC).
de Chiara C., Homšak M., Prosser G.A., Douglas H.L., Garza-Garcia A., Kelly G., Purkiss A.G., Tate E.W, & de Carvalho L.P. (2020). d-Cycloserine destruction by alanine racemase and the limit of irreversible inhibition. Nature chemical biology, 16(6), 686-694.
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7

Structural Analysis of LytM Domains

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The EnvC LytM domain (residues 290–419) was extracted using PyMOL (The PyMOL Molecular Graphics System, Version 1.8.4.0, Schrödinger, LLC) from the X-ray structure downloaded from the RCSB PDB database (Berman et al., 2000 (link)) (Uniprot ID: P37690, residues 278–419 PDB id: 4BH5 [Peters et al., 2013 (link)]). The 3D structures of NlpD (Uniprot ID: P0ADA3) and ActS (Uniprot ID: Q46798) were modeled using the Phyre web-server (Kelley et al., 2015 (link)) using PDB id: 6U2A (Shin et al., 2020 (link)) as template for both structures. The LytM domains of NlpD (residues 261–379) and ActS (residues 131–248) were then extracted using PyMOL (The PyMOL Molecular Graphics System, Version 1.8.4.0, Schrödinger, LLC).
Mueller E.A., Iken A.G., Öztürk M.A., Winkle M., Schmitz M., Vollmer W., Ventura B.D, & Levin P.A. (2021). The active repertoire of Escherichia coli peptidoglycan amidases varies with physiochemical environment. Molecular microbiology, 116(1), 311-328.
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8

Protein Structure Modeling Pipeline

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Models were built using Swiss-Model [41 (link)] and structures were visualized with PyMOL (PyMOL Molecular Graphics System, Version 1.5.0.4 Schrödinger, LLC). Homology modelling was supported by PSIPRED [42 (link)] and multisequence alignments were produced with MUSCLE [43 (link)]. Alignments and additional information of the models are provided in the respective legends.
Lemtiri-Chlieh F., Arold S.T, & Gehring C. (2020). Mg2+ is a Missing Link in Plant Cell Ca2+ Signalling and Homeostasis—A Study on Vicia faba Guard Cells. International Journal of Molecular Sciences, 21(11), 3771.
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9

Automated Crystallographic Data Collection and Processing

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All crystallographic data were collected in unattended mode, monitored by SynchWeb [31 (link)] at beamline I03 of the Diamond Light Source (DLS, Didcot, UK). Datasets were processed by autoPROC [32 (link)], data reduction and scaling were carried out using POINTLESS [33 (link)] and AIMLESS [34 (link)], respectively. The MRage molecular replacement pipeline [35 (link),36 (link)] was used to identify suitable search models (PDB accession codes 6ELS, 5CE9 and 4Z12) and to perform the initial molecular replacement search. Density modification was performed using Phenix AutoBuild [37 (link)], followed by interactive modelling in Coot [38 (link),39 (link)] to adjust for poorly fitted parts of the initial molecular replacement solution. The improved model was used for iterative density modification, chain rebuilding and extension, as well as for refinement in AutoBuild. Coot and Refmac5 [40 (link)] were applied for the final cycles of model-building and refinement. The occupancies of the copper ion binding sites were estimated and refined based on their anomalous contributions to the diffraction data. The data collection and refinement statistics are given in Table 1 and Table S2. All figures were prepared using the PyMol Molecular Graphics System (Version 2.5.2, Schrödinger, LLC).
Fekry M., Dave K.K., Badgujar D., Hamnevik E., Aurelius O., Dobritzsch D, & Danielson U.H. (2023). The Crystal Structure of Tyrosinase from Verrucomicrobium spinosum Reveals It to Be an Atypical Bacterial Tyrosinase. Biomolecules, 13(9), 1360.
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10

Crystallographic Structure Determination of FZD8-CRD

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Crystals
were flash-frozen by immersion in a reservoir solution supplemented
with 25% v/v glycerol followed by transferring to liquid nitrogen.
Data sets were recorded from crystals at 100 K at the Diamond Light
source (Didcot U.K., beamline I04-1) and processed with Xia2.61 (link) Structures were determined by molecular replacement
using Molrep (CCP4) using the previously reported FZD8CRD structure (PDB code 1IJY(14 (link))) as a search model. The
model was then manually built with COOT62 (link) and refined with Phenix. Data collection and refinement statistics
are shown in Table 1. We noticed that the Rfree for both of the structures
are relatively high, and we then used Zanuda63 (link) to check if the space group for each structure was misassigned;
refinement in lower symmetry space groups (P1 and P21 for the apo and complex structures, respectively)
did not result in significantly lower R factors and both structures
passed Zanuda tests. The PyMOL Molecular Graphics System (Schrödinger,
LLC.) was used for preparing figures.
Zhao Y., Ren J., Hillier J., Lu W, & Jones E.Y. (2020). Antiepileptic Drug Carbamazepine Binds to a Novel Pocket on the Wnt Receptor Frizzled-8. Journal of Medicinal Chemistry, 63(6), 3252-3260.
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