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Ligand Processing Module: Enhanced Identification and Comparison System Development

The Ligand Processing Module aims to streamline ligand identification and processing with various integrated tools, including Open Eye, VF.LIB, OpenBabel, and custom C++ code. This innovative system enhances the existing ligand validation process, providing features like graphical reporting, expanded search capabilities, and comparative analysis between 2D and 3D structures. Future developments include capturing detailed author refinement information and introducing a comprehensive user interface for editing and annotating ligand data. Current testing is underway by PDBe and RCSB, with significant updates planned.

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Ligand Processing Module: Enhanced Identification and Comparison System Development

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  1. D&A Common Tool – Ligand Processing Module Ligand Identification Dep CVS • Open Eye • VF LIB • Open Babel/ • Bali • In-house C++ code Existing Ligand 3 Ltr Code Validation Generate Graph* Level 1 Report UI Update Dep Data File New Ligand Annotation Filtered Dictionary Comparison 3 Ltr Code to Coordinate Comparison • Open Eye: Omega • & Flexi Chem • Corina • ACD Labs • CACTVS • In-house C++ code Update CCD *Future requirement: Capture full Author refinement dictionary (mmCIF), stereochem, picture etc, at deposition, to facilitate Ligand ID step CCD CVS Level 3 Edit UI Level 2 Expanded Search UI • In-house C++ code • Open Eye • VF LIB • Open Babel/Bali. 2D Structure Comparative output 3D Structure Upload to CVS’s is a “production” system obj., not to be implemented against the current systems. 3D Structure View 2D, 3D and Text integrated View (future enhancement) Super Ligand Proc. Chopper Additional search enhancement UI features TBD Merge Text Ligand File Editing August 18, 2010 MQ

  2. D&A Common Tool – Ligand Processing Module August Deliverable Status Update In test by PDBe and RCSB Ann. I0 Test V Simple Table format Ligand Identification • Open Eye • VF LIB • Open Babel/ • Bali • In-house C++ code Existing Ligand 3 Ltr Code Validation Generate Graph Level 1 Report UI Filtered Dictionary Comparison New Ligand Annotation 3 Ltr Code to Coordinate Comparison • Open Eye: Omega • & Flexi Chem • Corina • ACD Labs • CACTVS • In-house C++ code ZF: 1. exploring replacement of VF Lib with Eugene code. 2. Further enhance with Dohlc heuristics as appropriate. Existing code refactored to meet D&A Arch, code and modularity standards. Completed Aug 18. JW Level 2 Expanded Search UI Level 3 Edit UI • In-house C++ code • Open Eye • VF LIB • Open Babel/Bali. Raul S dev. UI’s as per req mock ups, according to SM model. ZF assisting with integration. Preview Aug 20, 1st pass (Level 1) deliverable Aug 27. ZF to complete integration by Aug 27 2D Structure Comparative output 3D Structure 3D Structure View Super Ligand Proc. Chopper DD DD: confirming requirements with RU Annotator grp Aug 19,20. Independent deliverable target for Aug 31. Merge Text Ligand File Editing August 18, 2010 MQ

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