An editor for the generation and customization of geometry restraints

Obtaining a restraint dictionary for novel ligands or improving restraints for known ligands can require their manual modification. This can be tedious and error-prone. REEL is a restraints editor that provides quick, easy and accurate development, allowing global changes and fine-tuning of individual restraints.

[1]  Rene Ranzinger,et al.  The GlycanBuilder and GlycoWorkbench glycoinformatics tools: updates and new developments , 2012, Biological chemistry.

[2]  Zukang Feng,et al.  The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank , 2015, Bioinform..

[3]  Martin Frank,et al.  EUROCarbDB: An open-access platform for glycoinformatics , 2010, Glycobiology.

[4]  Randy J. Read,et al.  Phenix - a comprehensive python-based system for macromolecular structure solution , 2012 .

[5]  R. Dwek,et al.  Glycobiology , 2018, Biochimie.

[6]  Károly Héberger,et al.  Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations? , 2015, Journal of Cheminformatics.

[7]  P. Karplus,et al.  Conformation‐dependent backbone geometry restraints set a new standard for protein crystallographic refinement , 2014, The FEBS journal.

[8]  良二 上田.  J. Appl. Cryst.の発刊に際して , 1970 .

[9]  Vladimir Prelog,et al.  Specification of Molecular Chirality , 1966 .

[10]  Dale E Tronrud,et al.  A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream , 2016, Acta crystallographica. Section D, Structural biology.

[11]  David Weininger,et al.  SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules , 1988, J. Chem. Inf. Comput. Sci..

[12]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[13]  Roland L. Dunbrack,et al.  Conformation dependence of backbone geometry in proteins. , 2009, Structure.

[14]  Alessio Ceroni,et al.  GlycoWorkbench: a tool for the computer-assisted annotation of mass spectra of glycans. , 2008, Journal of proteome research.

[15]  C. Lieth,et al.  GlycoCT-a unifying sequence format for carbohydrates. , 2008, Carbohydrate research.

[16]  P. Zwart,et al.  Towards automated crystallographic structure refinement with phenix.refine , 2012, Acta crystallographica. Section D, Biological crystallography.

[17]  Nathaniel Echols,et al.  The Phenix software for automated determination of macromolecular structures. , 2011, Methods.

[18]  O. Dym,et al.  Thermal stabilization of the protozoan Entamoeba histolytica alcohol dehydrogenase by a single proline substitution , 2008 .

[19]  Paul D Adams,et al.  Electronic Reprint Biological Crystallography Electronic Ligand Builder and Optimization Workbench (elbow ): a Tool for Ligand Coordinate and Restraint Generation Biological Crystallography Electronic Ligand Builder and Optimization Workbench (elbow): a Tool for Ligand Coordinate and Restraint Gener , 2022 .

[20]  P. Evans,et al.  An introduction to stereochemical restraints , 2006 .

[21]  Randy J. Read,et al.  Graphical tools for macromolecular crystallography in PHENIX , 2012, Journal of applied crystallography.

[22]  Martin Frank,et al.  GlycomeDB—a unified database for carbohydrate structures , 2010, Nucleic Acids Res..

[23]  J. Richardson,et al.  The penultimate rotamer library , 2000, Proteins.

[24]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[25]  김삼묘,et al.  “Bioinformatics” 특집을 내면서 , 2000 .