Tools for ligand validation in Coot

The current tools of Coot for ligand validation and comparison in are presented. The user-selected ligand is assessed by ligand-distortion and map-correlation metrics, and compared with those of ligands of the wwPDB to create a percentile rank.

[1]  Saulius Gražulis,et al.  AceDRG: a stereochemical description generator for ligands , 2017, Acta crystallographica. Section D, Structural biology.

[2]  Tjelvar S. G. Olsson,et al.  The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures , 2012, Journal of Computer-Aided Molecular Design.

[3]  Radka Svobodová Vareková,et al.  ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank , 2014, Nucleic Acids Res..

[4]  Karen Roberts,et al.  Structure-Guided Design of Highly Selective and Potent Covalent Inhibitors of ERK1/2. , 2015, Journal of medicinal chemistry.

[5]  F A Quiocho,et al.  Complexes of adenosine deaminase with two potent inhibitors: X-ray structures in four independent molecules at pH of maximum activity. , 1998, Biochemistry.

[6]  Paul Emsley,et al.  Handling ligands with Coot , 2012 .

[7]  Ian J. Tickle,et al.  Statistical quality indicators for electron-density maps , 2012, Acta crystallographica. Section D, Biological crystallography.

[8]  R. Rosenfeld.  Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[9]  Bernhard Rupp,et al.  Visualizing ligand molecules in Twilight electron density. , 2013, Acta crystallographica. Section F, Structural biology and crystallization communications.

[10]  Randy J. Read,et al.  A New Generation of Crystallographic Validation Tools for the Protein Data Bank , 2011, Structure.

[11]  Adrià Cereto-Massagué,et al.  The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites , 2013, Journal of Cheminformatics.

[12]  Haruki Nakamura,et al.  Announcing the worldwide Protein Data Bank , 2003, Nature Structural Biology.

[13]  N. Pannu,et al.  REFMAC5 for the refinement of macromolecular crystal structures , 2011, Acta crystallographica. Section D, Biological crystallography.

[14]  Audrey L Lamb,et al.  You are lost without a map: Navigating the sea of protein structures. , 2015, Biochimica et biophysica acta.

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

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

[17]  Jack Snoeyink,et al.  Nucleic Acids Research Advance Access published April 22, 2007 MolProbity: all-atom contacts and structure validation for proteins and nucleic acids , 2007 .

[18]  J. Richardson,et al.  Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. , 1999, Journal of molecular biology.

[19]  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..

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

[21]  Paul D. Adams,et al.  short communications Acta Crystallographica Section D Biological , 1998 .

[22]  Haruki Nakamura,et al.  Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. , 2016, Structure.

[23]  Jie Luo,et al.  Retrieval of Crystallographically-Derived Molecular Geometry Information , 2004, J. Chem. Inf. Model..

[24]  F. Young.  Biochemistry , 1955, The Indian Medical Gazette.

[25]  T. Jones,et al.  Between objectivity and subjectivity , 1990, Nature.

[26]  Manfred S. Weiss,et al.  Global indicators of X-ray data quality , 2001 .

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

[28]  G N Murshudov,et al.  Refinement of Atomic Structures Against cryo-EM Maps. , 2016, Methods in enzymology.

[29]  Alex M. Clark,et al.  2D Depiction of Protein-Ligand Complexes , 2007, J. Chem. Inf. Model..

[30]  Alexandre Urzhumtsev,et al.  EFRESOL: effective resolution of a diffraction data set , 2015 .

[31]  E. Dodson,et al.  The role of validation in macromolecular crystallography. , 1998, Acta crystallographica. Section D, Biological crystallography.

[32]  M. Zalis,et al.  Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. , 1999, Journal of molecular biology.