What is the proteinsplus server for?
ProteinsPlus structure-based modeling support server. This server is a common web portal for all tools related to structure-based modeling created by the AMD group (Prof. M. Rarey) at ZBH, Hamburg, including DoGSite Scorer, EDIA, PPI, PoseView, SIENA and ProToss
How to use proteinsplus tools?
The aim of ProteinsPlus (https://proteins.plus/) Server is to support life scientists in working with protein structures 1. Protein structures are the key for an understanding of function. They are an important resource in many biotechnological application areas from pharmaceutical research to biocatalysis.
What is the entry point to proteins Plus service?
16/04/2020 · MATERIALS AND METHODS—ENHANCEMENTS OF THE ProteinsPlus WEB SERVER Data handling. The entry point to the Proteins Plus service is in many cases a publicly available structure from the PDB... Structure validation and selection. Up to date, high quality data sets for the validation of structure-based ...
Where can I find the completed structures in protein plus?
Reference: Verification of protein structures: patterns of nonbonded atomic interactions, Colovos C and Yeates TO, 1993. C++ software. VERIFY 3D. Profile Search Software [Bowie et al., 1991, Luethy et al., 1992]. DSSP original and Wikipedia; PROVE. Reference: Deviations from standard atomic volumes as a quality measure for protein crystal structures, Pontius J, Richelle J, …
Why can't a ligand be converted to a potential water position?
Due to close contact with other ligand or protein atoms, some of the interaction surface may not be available and thus cannot be converted into potential water positions. Finally, all potential water positions that are position-optimized and merged in a self-assembling procedure.
What information is important regarding the formed hydrogen bonds to water molecules?
Additionally, important information regarding the formed hydrogen bonds to water molecules are summarized. If crystallographic water molecules were available in the starting structure, these water molecules will be used as a reference for the placed water molecules.
What are the two ligands of c-Abl?
The protein is human c-Abl tyrosine kinase, and the two ligands are imatinib (PDB entry 2hyy) and nilotinib (3cs9). The ligands and protein side chains are shown in ball-and-stick representation, with the ligand bonds coloured in purple.
What do the red circles and ellipses on a hydrogen bond mean?
The red circles and ellipses indicate protein residues that are in equivalent 3D positions when the two structural models are superposed. Improved DIMPLOT program.