Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution
暂无分享,去创建一个
Paul D. Adams | Nathaniel Echols | Ralf W. Grosse-Kunstleve | Pavel V. Afonine | Vincent B. Chen | Jeffrey J. Headd | Nigel W. Moriarty | David C. Richardson | Jane S. Richardson | J. Richardson | D. Richardson | P. Adams | J. Headd | N. Echols | P. Afonine | N. Moriarty | R. Grosse-Kunstleve | D. Richardson | Paul D. Adamsa | Jane S. Richardsonb | David C Richardson | Nathaniel Echols | Jane S Richardson | Paul D Adams | P. D. Adams
[1] Stephen Neidle,et al. Principles of nucleic acid structure , 2007 .
[2] Timothy Palzkill,et al. Co-Crystal Structures of PKG Iβ (92–227) with cGMP and cAMP Reveal the Molecular Details of Cyclic-Nucleotide Binding , 2011, PloS one.
[3] A. Brunger. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. , 1992 .
[4] Dale E Tronrud,et al. Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins. , 2010, Acta crystallographica. Section D, Biological crystallography.
[5] P. Bradley,et al. Toward High-Resolution de Novo Structure Prediction for Small Proteins , 2005, Science.
[6] J. Dennis,et al. Techniques for nonlinear least squares and robust regression , 1978 .
[7] Z Dauter,et al. 1.7 A structure of the stabilized REIv mutant T39K. Application of local NCS restraints. , 1999, Acta crystallographica. Section D, Biological crystallography.
[8] R J Read,et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.
[9] M. Zalis,et al. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. , 1999, Journal of molecular biology.
[10] N. Pannu,et al. REFMAC5 for the refinement of macromolecular crystal structures , 2011, Acta crystallographica. Section D, Biological crystallography.
[11] J. Richardson,et al. The penultimate rotamer library , 2000, Proteins.
[12] E. Westhof,et al. Geometric nomenclature and classification of RNA base pairs. , 2001, RNA.
[13] Axel T. Brunger,et al. X-PLOR Version 3.1: A System for X-ray Crystallography and NMR , 1992 .
[14] G J Kleywegt,et al. Phi/psi-chology: Ramachandran revisited. , 1996, Structure.
[15] R. Huber,et al. Accurate Bond and Angle Parameters for X-ray Protein Structure Refinement , 1991 .
[16] Brian W. Matthews,et al. An efficient general-purpose least-squares refinement program for macromolecular structures , 1987 .
[17] Conrad C. Huang,et al. UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..
[18] T J Oldfield,et al. A number of real-space torsion-angle refinement techniques for proteins, nucleic acids, ligands and solvent. , 2001, Acta crystallographica. Section D, Biological crystallography.
[19] Haruki Nakamura,et al. Announcing the worldwide Protein Data Bank , 2003, Nature Structural Biology.
[20] Richard Bertram,et al. An improved hydrogen bond potential: Impact on medium resolution protein structures , 2002, Protein science : a publication of the Protein Society.
[21] Ian W. Davis,et al. Structure validation by Cα geometry: ϕ,ψ and Cβ deviation , 2003, Proteins.
[22] Vincent B. Chen,et al. KING (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program , 2009, Protein science : a publication of the Protein Society.
[23] G J Kleywegt,et al. Model building and refinement practice. , 1997, Methods in enzymology.
[24] 良二 上田. J. Appl. Cryst.の発刊に際して , 1970 .
[25] Jeffrey J. Headd,et al. Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place , 2008, Journal of Structural and Functional Genomics.
[26] G. Sheldrick. A short history of SHELX. , 2008, Acta crystallographica. Section A, Foundations of crystallography.
[27] Vincent B. Chen,et al. Correspondence e-mail: , 2000 .
[28] G. Murshudov,et al. Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.
[29] A. Brunger. Version 1.2 of the Crystallography and NMR system , 2007, Nature Protocols.
[30] Glen E. Kellogg,et al. Applying an Empirical Hydropathic Forcefield in Refinement May Improve Low-Resolution Protein X-Ray Crystal Structures , 2011, PloS one.
[31] Paola Storici,et al. Structures of γ-Aminobutyric Acid (GABA) Aminotransferase, a Pyridoxal 5′-Phosphate, and [2Fe-2S] Cluster-containing Enzyme, Complexed with γ-Ethynyl-GABA and with the Antiepilepsy Drug Vigabatrin* , 2003, Journal of Biological Chemistry.
[32] W. Kabsch,et al. Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.
[33] Michael Levitt,et al. Super-resolution biomolecular crystallography with low-resolution data , 2010, Nature.
[34] R. Rosenfeld. Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.
[35] G. Kleywegt,et al. Checking your imagination: applications of the free R value. , 1996, Structure.
[36] Randy J. Read,et al. Acta Crystallographica Section D Biological , 2003 .
[37] George M. Church,et al. A structure-factor least-squares refinement procedure for macromolecular structures using constrained and restrained parameters , 1977 .
[38] Bradley J. Hintze,et al. ResDe: a new tool for visual definition of distance restraints for crystallographic refinement , 2010 .
[39] D. Richardson,et al. Exploring steric constraints on protein mutations using MAGE/PROBE , 2000, Protein science : a publication of the Protein Society.
[40] Nicholas Furnham,et al. Model-building strategies for low-resolution X-ray crystallographic data , 2009, Acta crystallographica. Section D, Biological crystallography.
[41] J. Richardson,et al. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. , 1999, Journal of molecular biology.
[42] P. Emsley,et al. Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.
[43] T. A. Jones,et al. Databases in protein crystallography. , 1998, Acta crystallographica. Section D, Biological crystallography.
[44] Fei Long,et al. REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. , 2004, Acta crystallographica. Section D, Biological crystallography.