Improvement of molecular-replacement models with Sculptor

The molecular-replacement model-improvement program Sculptor is described, with an analysis of the algorithms used.

[1]  Garib N. Murshudov,et al.  Model preparation in MOLREP and examples of model improvement using X-ray data , 2007, Acta crystallographica. Section D, Biological crystallography.

[2]  Fei Long,et al.  BALBES: a molecular-replacement pipeline , 2007, Acta crystallographica. Section D, Biological crystallography.

[3]  Norman Stein,et al.  CHAINSAW: a program for mutating pdb files used as templates in molecular replacement , 2008 .

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

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

[6]  Adam Godzik,et al.  The importance of alignment accuracy for molecular replacement. , 2004, Acta crystallographica. Section D, Biological crystallography.

[7]  M. O. Dayhoff,et al.  Atlas of protein sequence and structure , 1965 .

[8]  G. Kleywegt,et al.  Interactive motif and fold recognition in protein structures , 2002 .

[9]  P. Kraulis A program to produce both detailed and schematic plots of protein structures , 1991 .

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

[11]  Nam-Chul Ha,et al.  Crystal structure of a clip‐domain serine protease and functional roles of the clip domains , 2005, The EMBO journal.

[12]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[13]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[14]  Leszek Rychlewski,et al.  FFAS03: a server for profile–profile sequence alignments , 2005, Nucleic Acids Res..

[15]  Alexei Vagin,et al.  Molecular replacement with MOLREP. , 2010, Acta crystallographica. Section D, Biological crystallography.

[16]  Adam Godzik,et al.  The JCSG MR pipeline: optimized alignments, multiple models and parallel searches , 2007, Acta crystallographica. Section D, Biological crystallography.

[17]  Randy J. Read,et al.  Overview of the CCP4 suite and current developments , 2011, Acta crystallographica. Section D, Biological crystallography.

[18]  Peter J. Stuckey,et al.  MUSTANG-MR Structural Sieving Server: Applications in Protein Structural Analysis and Crystallography , 2010, PloS one.

[19]  E A Merritt,et al.  Raster3D: photorealistic molecular graphics. , 1997, Methods in enzymology.

[20]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[21]  P E Bourne,et al.  The Protein Data Bank. , 2002, Nucleic acids research.

[22]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[23]  A. Shrake,et al.  Environment and exposure to solvent of protein atoms. Lysozyme and insulin. , 1973, Journal of molecular biology.

[24]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[25]  S. Henikoff,et al.  Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Ronan M Keegan,et al.  Molecular replacement using ab initio polyalanine models generated with ROSETTA. , 2008, Acta crystallographica. Section D, Biological crystallography.

[27]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[28]  P. Bradley,et al.  High-resolution structure prediction and the crystallographic phase problem , 2007, Nature.

[29]  Ronan M Keegan,et al.  Automated search-model discovery and preparation for structure solution by molecular replacement. , 2007, Acta crystallographica. Section D, Biological crystallography.

[30]  S. McSweeney,et al.  Atomic resolution structures of trypsin provide insight into structural radiation damage. , 2001, Acta crystallographica. Section D, Biological crystallography.