Journal: ACS Synthetic Biology

Article Title: In Silico End-to-End Protein–Ligand Interaction Characterization Pipeline: The Case of SARS-CoV-2

doi: 10.1021/acssynbio.1c00368

Figure Lengend Snippet: PyMOL graphical user interface with PDB ID 6Y2G loaded.

Article Snippet: https://github.com/schrodinger/pymol-open-source : webpage on GitHub to download the Open-Source PyMOL version. https://pymol.org/2/support.html?#installation : webpage with PyMOL installation types required for different distributions (Windows, Linux, MacOSX). https://sourceforge.net/projects/pymol/lists/pymol-users : PyMOL Users Mailing List webpage, which includes the exchange of ideas, tips, and information with other knowledgeable users, as well as the update on the most recent PyMOL news. https://pymolwiki.org/index.php/Main_Page : PyMOLWiki webpage, which is a user knowledge database and could also guide the reader into tutorials, plugins or answers for questions often asked.

Techniques:

Journal: ACS Synthetic Biology

Article Title: In Silico End-to-End Protein–Ligand Interaction Characterization Pipeline: The Case of SARS-CoV-2

doi: 10.1021/acssynbio.1c00368

Figure Lengend Snippet: Object and selections names and menu items in GUI of PyMOL.

Article Snippet: https://github.com/schrodinger/pymol-open-source : webpage on GitHub to download the Open-Source PyMOL version. https://pymol.org/2/support.html?#installation : webpage with PyMOL installation types required for different distributions (Windows, Linux, MacOSX). https://sourceforge.net/projects/pymol/lists/pymol-users : PyMOL Users Mailing List webpage, which includes the exchange of ideas, tips, and information with other knowledgeable users, as well as the update on the most recent PyMOL news. https://pymolwiki.org/index.php/Main_Page : PyMOLWiki webpage, which is a user knowledge database and could also guide the reader into tutorials, plugins or answers for questions often asked.

Techniques:

Journal: ACS Synthetic Biology

Article Title: In Silico End-to-End Protein–Ligand Interaction Characterization Pipeline: The Case of SARS-CoV-2

doi: 10.1021/acssynbio.1c00368

Figure Lengend Snippet: Available molecular representations in PyMOL.

Article Snippet: https://github.com/schrodinger/pymol-open-source : webpage on GitHub to download the Open-Source PyMOL version. https://pymol.org/2/support.html?#installation : webpage with PyMOL installation types required for different distributions (Windows, Linux, MacOSX). https://sourceforge.net/projects/pymol/lists/pymol-users : PyMOL Users Mailing List webpage, which includes the exchange of ideas, tips, and information with other knowledgeable users, as well as the update on the most recent PyMOL news. https://pymolwiki.org/index.php/Main_Page : PyMOLWiki webpage, which is a user knowledge database and could also guide the reader into tutorials, plugins or answers for questions often asked.

Techniques:

Journal: ACS Synthetic Biology

Article Title: In Silico End-to-End Protein–Ligand Interaction Characterization Pipeline: The Case of SARS-CoV-2

doi: 10.1021/acssynbio.1c00368

Figure Lengend Snippet: Superposition of the lowest binding energy docking results of the 13b inhibitor obtained from ADT4 (in cyan), VINA (in yellow), and the X-ray structure (PDB ID: 6Y2G; pink) in the M pro binding site. The protein surface is colored in white, while the secondary structure of the protein chain A is represented in the green cartoon. The side chains of the most important residues found at the protein binding site are represented as green sticks. This figure was built and rendered using the program PyMOL.

Article Snippet: https://github.com/schrodinger/pymol-open-source : webpage on GitHub to download the Open-Source PyMOL version. https://pymol.org/2/support.html?#installation : webpage with PyMOL installation types required for different distributions (Windows, Linux, MacOSX). https://sourceforge.net/projects/pymol/lists/pymol-users : PyMOL Users Mailing List webpage, which includes the exchange of ideas, tips, and information with other knowledgeable users, as well as the update on the most recent PyMOL news. https://pymolwiki.org/index.php/Main_Page : PyMOLWiki webpage, which is a user knowledge database and could also guide the reader into tutorials, plugins or answers for questions often asked.

Techniques: Binding Assay, Protein Binding

Journal:

Article Title: Distal end of 105–125 Loop - a Putative Reductase Binding Domain of Phthalate Dioxygenase

doi: 10.1016/j.abb.2009.05.008

Figure Lengend Snippet: Amino acid arrangement in the vicinity of the [2Fe-2S] Rieske center of CarDO in its complex with Fdx (based on 2DE5). Fdx residues are shown in white, residues of CarDO subunits are shown in light blue if belonging to the same monomer as the Rieske center shown and in green if belonging to an adjacent oxygenase subunit. Conserved Trp 95 (Trp94 in PDO) is shown in yellow. A and B represent different views of the amino acids arrangement with A highlighting the interaction of Trp95 with the same subunit residues and B highlighting Trp95 interactions with residues from the adjacent oxygenase subunit. Dotted lines on B represent short range interactions (<4 Å) between selected residues. Figures were built in PyMOL 2006 from DeLano Scientific Inc., which incorporated Open-Source PyMOL 099rc6.

Article Snippet: Figures were built in PyMOL 2006 from DeLano Scientific Inc., which incorporated Open-Source PyMOL 099rc6.

Techniques: