ScienceDirect science article Simplified quality assessment for small molecule ligands in Feb 3 2022 To showcase the most interesting ligands in a PDB structure the RCSB org structure summary page of the entry highlights the ligand fitting quality to experimental
www4 rcsb org news 5764422099cccf72e74ca2cc Looking for Ligands rcsb org These searches will return a Ligand Summary page that contains an overview of the chemical component 2D and 3D images links to other resources and links to related
Ligand Expo Expo Home The Ligand Expo Tutorial contains a summary of query report and download features Select the Search menu to find a chemical component or build a new chemical component
RCSB PDB docs sequence viewers Sequence Annotations Viewer RCSB Oct 20 2024 Structure Summary Page Main Tab The Sequence Annotations Viewer in the Structure Summary Pages e g 4z35 displays the alignments between PDB Entity sequences and
PDB 101 small molecule ligands Small Molecule Ligands RCSB PDB 101 Figure 2 Description of small molecules ligands in PDB entry 1j1z as illustrated in an RCSB PDB Structure Summary page as of April 2017 This Small Molecules table compCardList image img display none compCardList image noscript img display block compCardList extra visibility hidden
Q4d Ligand Summary Page Rcsb Pdb
RCSB PDB ligand Q4D Q4D Ligand Summary Page RCSB PDB As a member of the wwPDB the RCSB PDB curates and annotates PDB data according to agreed upon standards The RCSB PDB also provides a variety of tools and resources
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National Center for Biotechnology Information pmc articles Simplified Quality Assessment for Small molecule Ligands in Feb 2 2022 Shao et al construct simplified PDB ligand quality composite ranking scores and implement the scores at RCSB org with easy to interpret 2D ligand quality plots allowing
Q4d Ligand Summary Page Rcsb Pdb
RCSB PDB docs exploring a 3d structure Ligands RCSB PDB The Interface Learning About The Structure Exploring Other Structures The Ligands tab displays the following plots and table for all validated non polymer ligands and indicate whether they are the ligands of interest LOI LOI is a functional ligand in macromolecular complexes designated as focus of research in the experiment by structure authors or by RCSB PDB under the criteria of 1 Formula Weight 150 Da and 2 Not in an exclusion list of likely non functional ligands as described in Ligand Validation In the Figure 1 for the PDB ID 7lad the 1 Top half of the page has 2D plots showing 2 Bottom half presents measures of ligand quality in instances of the ligand displayed in the 2D plots 3 Note for this structure there is no validation data available for the ligand XRD See full list on www rcsb org The experimental data fitting vs geometry 2D plot in the left presents ligand quality for all instances of the ligand in the structure The best instance is shown as a green diamond while all other instances are shown as green circles All other data on the ligands tab compares the quality of the ligand in the entry of interest in other structures See full list on www rcsb org The experimental data fitting vs geometry 2D plot in the left presents ligand quality for all instances of the ligand in the structure The best instance is shown as a green diamond while all other instances are shown as green circles All other data on the ligands tab compares the quality of the ligand in the entry of interest in other structures Various measures of fit to electron density and geometry of the ligand in other entries are presented in 2D plots and tabular format This analysis allows you to compare the ligand of interest in these structures to the same ligand in other structures either bound to the same or different targets and select the best instance s for visualization analysis and hypothesis development Learn more about the ligand validation process and measures All instances of the ligand of interest in the archive can be found from the Ligand Definition and Summary page by clicking on the button on the top right corner of the page See full list on www rcsb org
ACS Publications doi 10 RCSB Protein Data Bank A Resource for Chemical Biochemical Jan 6 2016 In this paper we describe data annotation practices and highlight RCSB PDB resources available for query and analysis and education People also search for
RCSB PDB ligand PDB PDB Ligand Summary Page RCSB PDB Oct 8 2009 As a member of the wwPDB the RCSB PDB curates and annotates PDB data according to agreed upon standards The RCSB PDB also provides a variety of tools and resources Formula C 15 H 12 Cl F 3 N 4 O Molecular Weight 356 73 Type NON POLYMER