Conformation‐dependent backbone geometry restraints set a new standard for protein crystallographic refinement
暂无分享,去创建一个
P. Karplus | P. Adams | D. Tronrud | N. Moriarty | P. Andrew Karplus | Nigel W. Moriarty | Dale E. Tronrud | Paul D. Adams
[1] R. Diamond,et al. A mathematical model-building procedure for proteins , 1966 .
[2] Peter Kramer,et al. An Efficient General-Purpose Least-Squares Refinement Program for Macromolecular Structures , 1987 .
[4] L. Schäfer,et al. Predictions of relative structural trends from ab initio derived standard geometry functions , 1986 .
[6] Roland L. Dunbrack,et al. Conformation dependence of backbone geometry in proteins. , 2009, Structure.
[7] Zbigniew Dauter,et al. Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them? , 2007, Acta crystallographica. Section D, Biological crystallography.
[8] Ian W. Davis,et al. Structure validation by Cα geometry: ϕ,ψ and Cβ deviation , 2003, Proteins.
[9] Dale E Tronrud,et al. A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution. , 2011, Acta crystallographica. Section D, Biological crystallography.
[10] Robert Huber,et al. Structure quality and target parameters , 2006 .
[11] Randy J. Read,et al. Graphical tools for macromolecular crystallography in PHENIX , 2012, Journal of applied crystallography.
[12] 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 .
[13] D. Baker,et al. Relaxation of backbone bond geometry improves protein energy landscape modeling , 2014, Protein science : a publication of the Protein Society.
[14] J. Deisenhofer,et al. Crystallographic refinement of the structure of bovine pancreatic trypsin inhibitor at l.5 Å resolution , 1975 .
[15] R. Berisio,et al. Interplay between Peptide Bond Geometrical Parameters in Nonglobular Structural Contexts , 2013, BioMed research international.
[16] Structural parameters for proteins derived from the atomic resolution (1.09 A) structure of a designed variant of the ColE1 ROP protein. , 1998, Acta crystallographica. Section D, Biological crystallography.
[17] Gert Vriend,et al. On the complexity of Engh and Huber refinement restraints: the angle τ as example , 2010, Acta crystallographica. Section D, Biological crystallography.
[18] R. Huber,et al. Accurate Bond and Angle Parameters for X-ray Protein Structure Refinement , 1991 .
[19] Nicholas Furnham,et al. Model-building strategies for low-resolution X-ray crystallographic data , 2009, Acta crystallographica. Section D, Biological crystallography.
[20] Randy J Read,et al. Automated structure solution with the PHENIX suite. , 2008, Methods in molecular biology.
[21] Roger L. Lundblad,et al. Handbook of Biochemistry and Molecular Biology, Fifth Edition , 2010 .
[22] G. Sheldrick. A short history of SHELX. , 2008, Acta crystallographica. Section A, Foundations of crystallography.
[23] David C. Richardson,et al. MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes , 2004, Nucleic Acids Res..
[24] K. D. Watenpaugh,et al. Refinement of the model of a protein: rubredoxin at 1.5 Å resolution , 1973 .
[25] Paul D. Adams,et al. Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution , 2012, Acta crystallographica. Section D, Biological crystallography.
[26] Vincent B. Chen,et al. Correspondence e-mail: , 2000 .
[27] Peter B. Krenesky,et al. Protein Geometry Database: a flexible engine to explore backbone conformations and their relationships to covalent geometry , 2009, Nucleic Acids Res..
[28] Randy J. Read,et al. A New Generation of Crystallographic Validation Tools for the Protein Data Bank , 2011, Structure.
[29] Roland L. Dunbrack,et al. Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites , 2011, Proceedings of the National Academy of Sciences.
[30] Roland L Dunbrack,et al. A forward-looking suggestion for resolving the stereochemical restraints debate: ideal geometry functions. , 2008, Acta crystallographica. Section D, Biological crystallography.
[31] Nathaniel Echols,et al. The Phenix software for automated determination of macromolecular structures. , 2011, Methods.
[32] L. Pauling,et al. The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. , 1951, Proceedings of the National Academy of Sciences of the United States of America.
[33] L. Schāfer,et al. Predictions of protein backbone bond distances and angles from first principles , 1995 .
[34] Zbigniew Dauter,et al. Numerology versus reality: a voice in a recent dispute. , 2007, Acta crystallographica. Section D, Biological crystallography.
[35] A. Wlodawer,et al. Proteins do not have strong spines after all. , 2009, Structure.
[36] Randy J. Read,et al. Acta Crystallographica Section D Biological , 2003 .
[37] Randy J. Read,et al. Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum , 2012, Acta crystallographica. Section D, Biological crystallography.
[38] Dale E Tronrud,et al. Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins. , 2010, Acta crystallographica. Section D, Biological crystallography.
[39] Fei Long,et al. REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. , 2004, Acta crystallographica. Section D, Biological crystallography.
[40] K. Dill,et al. The flexibility in the proline ring couples to the protein backbone , 2005, Protein science : a publication of the Protein Society.
[41] 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.
[42] W. Hendrickson. Stereochemically restrained refinement of macromolecular structures. , 1985, Methods in enzymology.
[43] B. Matthews,et al. A method of obtaining a stereochemically acceptable protein model which fits a set of atomic coordinates , 1976 .
[44] J. Konnert,et al. A restrained-parameter structure-factor least-squares refinement procedure for large asymmetric units , 1976 .
[45] Full-matrix refinement of the protein crambin at 0.83 A and 130 K. , 1995, Acta crystallographica. Section D, Biological crystallography.
[46] N. W. Isaacs,et al. A method for fitting satisfactory models to sets of atomic positions in protein structure refinements , 1976 .
[47] P. Karplus. Experimentally observed conformation‐dependent geometry and hidden strain in proteins , 1996, Protein science : a publication of the Protein Society.
[48] H. Witte. Tables of Interatomic Distances and Configuration in Molecules and Ions. , 1959 .
[49] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[50] L. E. Sutton,et al. Tables of interatomic distances and configuration in molecules and ions , 1958 .
[51] Brian W. Matthews,et al. An efficient general-purpose least-squares refinement program for macromolecular structures , 1987 .