An approach to creating a more realistic working model from a protein data bank entry
暂无分享,去创建一个
James J. P. Stewart | J. Stewart | Sonja B. Braun-Sand | Benjamin P. Martin | Christopher J. Brandon | Kelly J. McGee | Kelly J McGee
[1] A. Leach. Molecular Modelling: Principles and Applications , 1996 .
[2] Ashwini Nangia,et al. Conformational polymorphism in organic crystals. , 2008, Accounts of chemical research.
[3] C. Sander,et al. Errors in protein structures , 1996, Nature.
[4] Vincent B. Chen,et al. Correspondence e-mail: , 2000 .
[5] Randy J. Read,et al. A New Generation of Crystallographic Validation Tools for the Protein Data Bank , 2011, Structure.
[6] J. Nielsen,et al. The pKa Cooperative: A collaborative effort to advance structure‐based calculations of pKa values and electrostatic effects in proteins , 2011, Proteins.
[7] Haruki Nakamura,et al. Announcing the worldwide Protein Data Bank , 2003, Nature Structural Biology.
[8] S. Ramakumar,et al. The occurrence of CH…O hydrogen bonds in α‐helices and helix termini in globular proteins , 2004, Proteins.
[9] T. Jones,et al. Between objectivity and subjectivity , 1990, Nature.
[10] Brendan Borrell,et al. Fraud rocks protein community , 2009, Nature.
[11] R. Kretsinger,et al. Refinement of the structure of carp muscle calcium-binding parvalbumin by model building and difference Fourier analysis. , 1976, Journal of molecular biology.
[12] Anastassis Perrakis,et al. Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank , 2011, Bioinform..
[13] Arieh Warshel,et al. Simulating electrostatic energies in proteins: Perspectives and some recent studies of pKas, redox, and other crucial functional properties , 2011, Proteins.
[14] V Lamzin,et al. Accurate protein crystallography at ultra-high resolution: valence electron distribution in crambin. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[15] Randy J. Read,et al. Crystallography: Crystallographic evidence for deviating C3b structure , 2007, Nature.
[16] Robert Huber,et al. Structure quality and target parameters , 2006 .
[17] Charles L Brooks,et al. Recent advances in implicit solvent-based methods for biomolecular simulations. , 2008, Current opinion in structural biology.
[18] B. García-Moreno E.,et al. Structural interpretation of pH and salt-dependent processes in proteins with computational methods. , 2004, Methods in enzymology.
[19] Randy J. Read,et al. Acta Crystallographica Section D Biological , 2003 .
[20] J. Shankar,et al. PRINCIPLES OF PROTEIN CRYSTALLIZATION , 2013 .
[21] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[22] Conrad C. Huang,et al. UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..
[23] Saraswathi Vishveshwara,et al. Short hydrogen bonds in proteins , 2005, The FEBS journal.
[24] G. Murshudov,et al. Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.
[25] Kenneth M Merz,et al. Refinement of protein crystal structures using energy restraints derived from linear-scaling quantum mechanics. , 2005, Acta crystallographica. Section D, Biological crystallography.
[26] Vincent Breton,et al. PDB_REDO: automated re-refinement of X-ray structure models in the PDB , 2009, Journal of applied crystallography.
[27] Ar Lang,et al. International Tables for Crystallography, Vol C , 1992 .
[28] James J. P. Stewart,et al. Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters , 2012, Journal of Molecular Modeling.
[29] F. Allen. The Cambridge Structural Database: a quarter of a million crystal structures and rising. , 2002, Acta crystallographica. Section B, Structural science.
[30] G. Desiraju. The C-H×××O Hydrogen Bond: Structural Implications and Supramolecular Design , 1996 .
[31] R. Huber,et al. Accurate Bond and Angle Parameters for X-ray Protein Structure Refinement , 1991 .
[32] Gerard J Kleywegt,et al. Limitations and lessons in the use of X-ray structural information in drug design , 2008, Drug Discovery Today.
[33] G. Chang,et al. Structure of the ABC Transporter MsbA in Complex with ADP·Vanadate and Lipopolysaccharide , 2005, Science.
[34] Olga Kennard,et al. Systematic analysis of structural data as a research technique in organic chemistry , 1983 .
[35] T. Hahn. International tables for crystallography , 2002 .
[36] Raymond C Stevens,et al. Retraction: Cocrystal structure of synaptobrevin-II bound to botulinum neurotoxin type B at 2.0 Å resolution , 2009, Nature Structural &Molecular Biology.
[37] Kurt Wüthrich,et al. NMR analysis of a 900K GroEL–GroES complex , 2002, Nature.