The PDB_REDO server for macromolecular structure model optimization
暂无分享,去创建一个
Fei Long | Robbie P. Joosten | Anastassis Perrakis | Garib N. Murshudov | G. Murshudov | F. Long | R. Joosten | A. Perrakis
[1] C. Sander,et al. Errors in protein structures , 1996, Nature.
[2] Haruki Nakamura,et al. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data , 2006, Nucleic Acids Res..
[3] C. Sander,et al. Quality control of protein models : directional atomic contact analysis , 1993 .
[4] 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.
[5] Z. Otwinowski,et al. [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.
[6] R. Fisher. FREQUENCY DISTRIBUTION OF THE VALUES OF THE CORRELATION COEFFIENTS IN SAMPLES FROM AN INDEFINITELY LARGE POPU;ATION , 1915 .
[7] Anastassis Perrakis,et al. Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank , 2011, Bioinform..
[8] Gert Vriend,et al. PDB Improvement Starts with Data Deposition , 2007, Science.
[9] Michael Krug,et al. XDSAPP: a graphical user interface for the convenient processing of diffraction data using XDS , 2012 .
[10] Ronan M Keegan,et al. Automated search-model discovery and preparation for structure solution by molecular replacement. , 2007, Acta crystallographica. Section D, Biological crystallography.
[11] Graeme Winter,et al. Decision making in xia2 , 2013, Acta crystallographica. Section D, Biological crystallography.
[12] Randy J. Read,et al. Dauter Iterative model building , structure refinement and density modification with the PHENIX AutoBuild wizard , 2007 .
[13] R. Rosenfeld. Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.
[14] Victor S Lamzin,et al. Auto-rickshaw: an automated crystal structure determination platform as an efficient tool for the validation of an X-ray diffraction experiment. , 2005, Acta crystallographica. Section D, Biological crystallography.
[15] 良二 上田. J. Appl. Cryst.の発刊に際して , 1970 .
[16] G. G. Stokes. "J." , 1890, The New Yale Book of Quotations.
[17] Ian J. Tickle,et al. Statistical quality indicators for electron-density maps , 2012, Acta crystallographica. Section D, Biological crystallography.
[18] Thomas R Ioerger,et al. Automatic modeling of protein backbones in electron-density maps via prediction of Calpha coordinates. , 2002, Acta crystallographica. Section D, Biological crystallography.
[19] J. Zou,et al. Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.
[20] Kevin Cowtan,et al. research papers Acta Crystallographica Section D Biological , 2005 .
[21] N. Pannu,et al. REFMAC5 for the refinement of macromolecular crystal structures , 2011, Acta crystallographica. Section D, Biological crystallography.
[22] M. Braga,et al. Exploratory Data Analysis , 2018, Encyclopedia of Social Network Analysis and Mining. 2nd Ed..
[23] R. Dennis Cook,et al. Cross-Validation of Regression Models , 1984 .
[24] Chris Sander,et al. Objectively judging the quality of a protein structure from a Ramachandran plot , 1997, Comput. Appl. Biosci..
[25] C Sander,et al. The use of position‐specific rotamers in model building by homology , 1995, Proteins.
[26] Gert Vriend,et al. Increasing the precision of comparative models with YASARA NOVA—a self‐parameterizing force field , 2002, Proteins.
[27] Randy J. Read,et al. A New Generation of Crystallographic Validation Tools for the Protein Data Bank , 2011, Structure.
[28] G. N. Ramachandran,et al. Stereochemistry of polypeptide chain configurations. , 1963, Journal of molecular biology.
[29] Tom Alber,et al. Automated protein crystal structure determination using ELVES. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[30] Clemens Vonrhein,et al. Data processing and analysis with the autoPROC toolbox , 2011, Acta crystallographica. Section D, Biological crystallography.
[31] G. Kleywegt,et al. Checking your imagination: applications of the free R value. , 1996, Structure.
[32] Randy J. Read,et al. Phaser crystallographic software , 2007, Journal of applied crystallography.
[33] Claus-Wilhelm von der Lieth,et al. pdb-care (PDB CArbohydrate REsidue check): a program to support annotation of complex carbohydrate structures in PDB files , 2004, BMC Bioinformatics.
[34] K. Pearson,et al. Biometrika , 1902, The American Naturalist.
[35] P. Andrew Karplus,et al. Linking Crystallographic Model and Data Quality , 2012, Science.
[36] P. Emsley,et al. Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.
[37] Fei Long,et al. BALBES: a molecular-replacement pipeline , 2007, Acta crystallographica. Section D, Biological crystallography.
[38] G J Williams,et al. The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.
[39] Randy J. Read,et al. Overview of the CCP4 suite and current developments , 2011, Acta crystallographica. Section D, Biological crystallography.
[40] L. Serrano,et al. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. , 2002, Journal of molecular biology.
[41] A. Brunger. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. , 1992 .
[42] G. Murshudov,et al. Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.
[43] Vincent Breton,et al. PDB_REDO: automated re-refinement of X-ray structure models in the PDB , 2009, Journal of applied crystallography.
[44] I. Tickle,et al. Experimental determination of optimal root-mean-square deviations of macromolecular bond lengths and angles from their restrained ideal values. , 2007, Acta crystallographica. Section D, Biological crystallography.
[45] 김삼묘,et al. “Bioinformatics” 특집을 내면서 , 2000 .
[46] T. Jones,et al. Between objectivity and subjectivity , 1990, Nature.
[47] Keehyoung Joo,et al. Improving physical realism, stereochemistry, and side‐chain accuracy in homology modeling: Four approaches that performed well in CASP8 , 2009, Proteins.
[48] Randy J. Read,et al. Electronic Reprint Biological Crystallography Decision-making in Structure Solution Using Bayesian Estimates of Map Quality: the Phenix Autosol Wizard Biological Crystallography Decision-making in Structure Solution Using Bayesian Estimates of Map Quality: the Phenix Autosol Wizard , 2022 .
[49] Jan Pieter Abrahams,et al. Recent advances in the CRANK software suite for experimental phasing , 2011, Acta crystallographica. Section D, Biological crystallography.
[50] Kevin Cowtan,et al. The Buccaneer software for automated model building. 1. Tracing protein chains. , 2006, Acta crystallographica. Section D, Biological crystallography.
[51] Olof Svensson,et al. Automatic processing of macromolecular crystallography X-ray diffraction data at the ESRF , 2013, Journal of applied crystallography.
[52] BMC Bioinformatics , 2005 .
[53] Krista Joosten,et al. PDB_REDO: constructive validation, more than just looking for errors , 2012, Acta crystallographica. Section D, Biological crystallography.
[54] Anastassis Perrakis,et al. Automated protein model building combined with iterative structure refinement , 1999, Nature Structural Biology.
[55] Markus Kroemer,et al. APRV - a program for automated data processing, refinement and visualization. , 2004, Acta crystallographica. Section D, Biological crystallography.
[56] Zhong Ren,et al. Automated crystallographic system for high-throughput protein structure determination. , 2003, Acta crystallographica. Section D, Biological crystallography.