G. Murshudov

发表

Refinement of macromolecular structures by the maximum-likelihood method.

G. Murshudov, A. Vagin, E. Dodson, 1997, Acta crystallographica. Section D, Biological crystallography.

High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy☆

R. Henderson, S. Scheres, G. McMullan, 2013, Ultramicroscopy.

REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use.

Fei Long, Stuart McNicholas, Liz Potterton, 2004, Acta crystallographica. Section D, Biological crystallography.

Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions

Alan Brown, Fei Long, Robert A. Nicholls, 2015, Acta crystallographica. Section D, Biological crystallography.

Use of TLS parameters to model anisotropic displacements in macromolecular refinement.

G N Murshudov, M D Winn, G. Murshudov, 2001, Acta crystallographica. Section D, Biological crystallography.

Macromolecular TLS refinement in REFMAC at moderate resolutions.

Martyn D Winn, Garib N Murshudov, Miroslav Z Papiz, 2003, Methods in enzymology.

REFMAC5 for the refinement of macromolecular crystal structures

N. Pannu, G. Murshudov, A. Vagin, 2011, Acta crystallographica. Section D, Biological crystallography.

Efficient anisotropic refinement of macromolecular structures using FFT.

K. Wilson, G. Murshudov, A. Vagin, 1999, Acta crystallographica. Section D, Biological crystallography.

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.

Haruki Nakamura, Evan Bolton, Zukang Feng, 2016, Structure.

Incorporation of prior phase information strengthens maximum-likelihood structure refinement.

G N Murshudov, R J Read, E J Dodson, 1998, Acta crystallographica. Section D, Biological crystallography.

The polypeptide chain fold in tyrosine phenol‐lyase, a pyridoxal‐5′‐phosphate‐dependent enzyme

Z. Dauter, K. Wilson, A. Antson, 1992, FEBS letters.

Pathological macromolecular crystallographic data affected by twinning, partial-disorder and exhibiting multiple lattices for testing of data processing and refinement tools

S. Phillips, G. Murshudov, E. Lowe, 2018, Scientific Reports.

Surprises and pitfalls arising from (pseudo)symmetry

P. Zwart, P. Adams, G. Murshudov, 2007, Acta crystallographica. Section D, Biological crystallography.

Robust background modelling in DIALS

Gwyndaf Evans, James M. Parkhurst, Luis Fuentes-Montero, 2016, Journal of applied crystallography.

DNA Topoisome Trapping a DNA in Motion

G. Murshudov, B. Bax, Maxwell, 2019 .

DNA Topoisomerase Inhibitors: Trapping a DNA-Cleaving Machine in Motion

G. Murshudov, A. Maxwell, B. Bax, 2019, Journal of molecular biology.

Cryo-EM structures of Tau filaments from Alzheimer’s disease brain

A. Murzin, B. Ghetti, R. Crowther, 2017, Nature.

How to tackle protein structural data from solution and solid state: An integrated approach.

C. Luchinat, G. Murshudov, E. Ravera, 2016, Progress in nuclear magnetic resonance spectroscopy.

The structure of the cofactor-binding fragment of the LysR family member, CysB: a familiar fold with a surprising subunit arrangement.

G N Murshudov, E J Dodson, C Addy, 1997, Structure.

Single-particle cryo-EM at atomic resolution

S. Scheres, G. McMullan, G. Murshudov, 2020, Nature.

Structural characterization of Helicobacter pylori dethiobiotin synthetase reveals differences between family members

A. Edwards, G. Murshudov, W. Minor, 2012, The FEBS journal.

Structure of the Bacillus cell fate determinant SpoIIAA in phosphorylated and unphosphorylated forms.

A. Wilkinson, G. Murshudov, R. Lewis, 2001, Structure.

Local and global analysis of macromolecular atomic displacement parameters

G. Murshudov, R. C. Masmaliyeva, Kave H Babai, 2020, bioRxiv.

Conformation-independent structural comparison of macromolecules with ProSMART

G. Murshudov, M. Fischer, S. McNicholas, 2014, Acta crystallographica. Section D, Biological crystallography.

Low-resolution refinement tools in REFMAC5

Fei Long, Garib N. Murshudov, Robert A. Nicholls, 2012, Acta crystallographica. Section D, Biological crystallography.

“Conditional Restraints”: Restraining the Free Atoms in ARP/wARP

Serge X. Cohen, W. Mooij, G. Murshudov, 2009, Structure.

Substrate distortion by a beta-mannanase: snapshots of the Michaelis and covalent-intermediate complexes suggest a B(2,5) conformation for the transition state.

S. Withers, D. Stoll, G. Murshudov, 2002, Angewandte Chemie.

The structures and electronic configuration of compound I intermediates of Helicobacter pylori and Penicillium vitale catalases determined by X-ray crystallography and QM/MM density functional theory calculations.

G. Murshudov, M. Alfonso-Prieto, C. Rovira, 2007, Journal of the American Chemical Society.

Interdigitated immunoglobulin arrays form the hyperstable surface layer of the extremophilic bacterium Deinococcus radiodurans

T. Bharat, G. Murshudov, E. Tocheva, 2022, bioRxiv.

Tools for Refinement against Low Resolution X-ray Data and Fit to EM Reconstructions

P. Emsley, G. Murshudov, F. Long, 2014 .

SOME PROPERTIES OF CRYSTALLOGRAPHIC RELIABILITY INDEX - Rfactor: EFFECTO OF TWINNING

G. Murshudov, 2011 .

The structure of NADH in the enzyme dTDP-d-glucose dehydratase (RmlB).

D. Philp, J. Naismith, G. Murshudov, 2003, Journal of the American Chemical Society.

Stabilizing bound O2 in myoglobin by valine68 (E11) to asparagine substitution.

S. Krzywda, M. Jaskólski, A. Wilkinson, 1998, Biochemistry.

How good are my data and what is the resolution?

Philip R. Evans, Garib N. Murshudov, P. Evans, 2013, Acta crystallographica. Section D, Biological crystallography.

Overview of the CCP4 suite and current developments

Randy J. Read, Martyn D. Winn, Eleanor J. Dodson, 2011, Acta crystallographica. Section D, Biological crystallography.

Structure of the Yeast Mitochondrial Large Ribosomal Subunit

Alan Brown, Fei Long, V. Ramakrishnan, 2014, Science.

Crystal structure of dodecameric vanadium-dependent bromoperoxidase from the red algae Corallina officinalis.

G. Murshudov, J. Littlechild, M. Isupov, 2000, Journal of molecular biology.

Crystal structure of GerE, the ultimate transcriptional regulator of spore formation in Bacillus subtilis.

G N Murshudov, E J Dodson, G. Leonard, 2001, Journal of molecular biology.

Data mining of iron(II) and iron(III) bond-valence parameters, and their relevance for macromolecular crystallography

Frank H. Allen, Heping Zheng, Wladek Minor, 2017, Acta crystallographica. Section D, Structural biology.

The missing link: covalent linkages in structural models

P. Emsley, G. Murshudov, M. Fischer, 2021, Acta crystallographica. Section D, Structural biology.

Structural origins of the functional divergence of human insulin-like growth factor-I and insulin.

Z. Dauter, G. Murshudov, E. Dodson, 2002, Biochemistry.

Structure of a slow processing precursor penicillin acylase from Escherichia coli reveals the linker peptide blocking the active-site cleft.

K. Wilson, G. Murshudov, C. Verma, 2000, Journal of molecular biology.

Direct incorporation of experimental phase information in model refinement.

Pavol Skubák, Navraj S Pannu, Garib N Murshudov, 2004, Acta crystallographica. Section D, Biological crystallography.

Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM

Garib N Murshudov, Robert A Nicholls, Oleg Kovalevskiy, 2018, Acta crystallographica. Section D, Structural biology.

Structure of the Heme d of Penicillium vitale and Escherichia coli Catalases (*)

B. Vainshtein, Z. Dauter, J. Bravo, 1996, The Journal of Biological Chemistry.

Cryo-EM single particle structure refinement and map calculation using Servalcat

Colin M. Palmer, G. Murshudov, K. Yamashita, 2021, bioRxiv.

JLigand: a graphical tool for the CCP4 template-restraint library

Garib N. Murshudov, G. Murshudov, A. Vagin, 2012, Acta crystallographica. Section D, Biological crystallography.

Structure of the large ribosomal subunit from human mitochondria

Alan Brown, V. Ramakrishnan, Sjors H. W. Scheres, 2014, Science.

Bipartite binding and partial inhibition links DEPTOR and mTOR in a mutually antagonistic embrace

Roger L. Williams, G. Murshudov, S. Freund, 2021, bioRxiv.

The PDB_REDO server for macromolecular structure model optimization

Fei Long, Robbie P. Joosten, Anastassis Perrakis, 2014, IUCrJ.

ARP/wARP and molecular replacement: the next generation

Fei Long, Serge X. Cohen, Anastassis Perrakis, 2007, Acta crystallographica. Section D, Biological crystallography.

MutS/MutL crystal structure reveals that the MutS sliding clamp loads MutL onto DNA

J. Lebbink, H. Winterwerp, T. Sixma, 2015, eLife.

Who checks the checkers? Four validation tools applied to eight atomic resolution structures. EU 3-D Validation Network.

Chris Sander, Shoshana J. Wodak, Jean Richelle, 1998, Journal of molecular biology.

Structures of filaments from Pick’s disease reveal a novel tau protein fold

Alexey G. Murzin, Sjors H.W. Scheres, Bernardino Ghetti, 2018, Nature.

Single-particle cryo-EM at atomic resolution

Takanori Nakane, Dimitri Y. Chirgadze, Tomas Malinauskas, 2020, Nature.

The structural basis of sequence-independent peptide binding by OppA protein.

G N Murshudov, E J Dodson, G G Dodson, 1994, Science.

Initiation of Translation by Cricket Paralysis Virus IRES Requires Its Translocation in the Ribosome

V. Ramakrishnan, Israel S. Fernández, Garib Murshudov, 2014, Cell.

Structures of actin-like ParM filaments show architecture of plasmid-segregating spindles

C. Sachse, T. Bharat, J. Löwe, 2015, Nature.

3D-Strudel - a novel model-dependent map-feature validation method for high-resolution cryo-EM structures

G. Kleywegt, A. Patwardhan, G. Murshudov, 2021, bioRxiv.

EMDA: A Python package for Electron Microscopy Data Analysis

G. Murshudov, K. Yamashita, R. Warshamanage, 2021, bioRxiv.

Developments in the CCP4 molecular-graphics project.

Anastassis Perrakis, Eugene Krissinel, Kevin Cowtan, 2004, Acta crystallographica. Section D, Biological crystallography.

BALBES: a molecular-replacement pipeline

Fei Long, Garib N. Murshudov, Alexei A. Vagin, 2007, Acta crystallographica. Section D, Biological crystallography.

The three-dimensional structure of a Trichoderma reesei beta-mannanase from glycoside hydrolase family 5.

G Murshudov, K S Wilson, M Penttilä, 2000, Acta crystallographica. Section D, Biological crystallography.

Overview of refinement procedures within REFMAC5: utilizing data from different sources

Fei Long, Garib N Murshudov, Azzurra Carlon, 2018, Acta crystallographica. Section D, Structural biology.

Fisher's information in maximum-likelihood macromolecular crystallographic refinement.

Garib N Murshudov, Andrey A Lebedev, G. Murshudov, 2003, Acta crystallographica. Section D, Biological crystallography.

X-ray structure of bovine pancreatic phospholipase A2 at atomic resolution.

K. H. Kalk, B. Dijkstra, K. Wilson, 2001, Acta crystallographica. Section D, Biological crystallography.

The three-dimensional structure of human S100A12.

K. Wilson, A. Antson, G. Murshudov, 2001, Acta crystallographica. Section D, Biological crystallography.

Three‐dimensional structure of catalase from Micrococcus lysodeikticus at 1.5 Å resolution

B. Vainshtein, Z. Dauter, K. Wilson, 1992, FEBS letters.

The structures of Micrococcus lysodeikticus catalase, its ferryl intermediate (compound II) and NADPH complex.

Zbigniew Dauter, Keith S Wilson, Garib N Murshudov, 2002, Acta crystallographica. Section D, Biological crystallography.

Model preparation in MOLREP and examples of model improvement using X-ray data

Garib N. Murshudov, Alexei A. Vagin, G. Murshudov, 2007, Acta crystallographica. Section D, Biological crystallography.

PDB_REDO: constructive validation, more than just looking for errors

Krista Joosten, Robbie P. Joosten, Anastassis Perrakis, 2012, Acta crystallographica. Section D, Biological crystallography.

Validation tools: can they indicate the information content of macromolecular crystal structures?

G N Murshudov, G J Davies, E J Dodson, 1998, Structure.

Background modelling of diffraction data in the presence of ice rings

Gwyndaf Evans, James M Parkhurst, Andrea Thorn, 2017, IUCrJ.

Structural Flexibility of the Macrophage Dengue Virus Receptor CLEC5A

G. Screaton, G. Murshudov, A. Vagin, 2011, The Journal of Biological Chemistry.

AceDRG: a stereochemical description generator for ligands

Saulius Gražulis, Fei Long, Andrius Merkys, 2017, Acta crystallographica. Section D, Structural biology.

The crystal structures of the oligopeptide-binding protein OppA complexed with tripeptide and tetrapeptide ligands.

C. Higgins, J. Tame, A. Wilkinson, 1995, Structure.

Automated refinement of macromolecular structures at low resolution using prior information

Garib N. Murshudov, Robert A. Nicholls, Oleg Kovalevskiy, 2016, Acta crystallographica. Section D, Structural biology.

Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB).

Masashi Yokochi, Genji Kurisu, Zukang Feng, 2019, Acta crystallographica. Section D, Structural biology.

BLANC: the program suite for protein crystallography

Garib N. Murshudov, Alexei A. Vagin, B. V. Strokopytov, 1998 .

Validation and extraction of molecular-geometry information from small-molecule databases

Saulius Gražulis, Fei Long, Andrius Merkys, 2017, Acta crystallographica. Section D, Structural biology.

Binding of non-catalytic ATP to human hexokinase I highlights the structural components for enzyme-membrane association control.

M. Bolognesi, G. Murshudov, C. Rosano, 1999, Structure.

Evaluating the solution from MrBUMP and BALBES

Martyn D. Winn, Fei Long, Vincent J. Fazio, 2011 .

The structure of the exo-beta-(1,3)-glucanase from Candida albicans in native and bound forms: relationship between a pocket and groove in family 5 glycosyl hydrolases.

S M Cutfield, G J Davies, G Murshudov, 1999, Journal of molecular biology.

Cryo-EM single-particle structure refinement and map calculation using Servalcat

Colin M. Palmer, G. Murshudov, K. Yamashita, 2021, Acta crystallographica. Section D, Structural biology.

Refinement of Atomic Structures Against cryo-EM Maps.

G N Murshudov, G. Murshudov, 2016, Methods in enzymology.

On the complementarity of X-ray and NMR data

C. Luchinat, G. Murshudov, V. Calderone, 2020, Journal of structural biology: X.

SPINE workshop on automated X-ray analysis: a progress report.

G N Murshudov, A Muller, K D Cowtan, 2006, Acta crystallographica. Section D, Biological crystallography.

Joint X-ray/NMR structure refinement of multidomain/multisubunit systems

C. Luchinat, G. Murshudov, E. Ravera, 2018, Journal of Biomolecular NMR.

Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences

Claudio Luchinat, Vito Calderone, Giacomo Parigi, 2014, Acta crystallographica. Section D, Biological crystallography.

NMR trial models: experiences with the colicin immunity protein Im7 and the p85alpha C-terminal SH2-peptide complex.

A. Breeze, G. Murshudov, D. Derbyshire, 2001, Acta crystallographica. Section D, Biological crystallography.

Modelling covalent linkages in CCP4

P. Emsley, G. Murshudov, M. Fischer, 2021, Acta crystallographica. Section D, Structural biology.

Automated refinement of low-resolution macromolecular structures using prior information

G. Murshudov, R. Nicholls, O. Kovalevskiy, 2015 .

Structures of Plasmodium falciparum purine nucleoside phosphorylase complexed with sulfate and its natural substrate inosine.

J. Luft, W. Hol, A. Wilkinson, 2005, Acta crystallographica. Section D, Biological crystallography.

Low-resolution refinement in the program REFMAC

G. N. Murshudov, G. Murshudov, 2011 .

Crystal structure of an extracellular fragment of the rat CD4 receptor containing domains 3 and 4.

G. Murshudov, A. Barclay, J. Turkenburg, 1994, Structure.

Description of program using maximum likelihood residual for macromolecular refinement, illustrated by several examples

G. Murshudov, E. Dodson, A. Vagin, 1996 .

A redox switch allows binding of Fe(II) and Fe(III) ions in the cyanobacterial iron binding protein FutA from Prochlorococcus

G. Murshudov, I. Tews, J. Worrall, 2023, bioRxiv.

DNA variability in five crystal structures of d(CGCAATTGCG).

G. Murshudov, R. Steiner, J. A. Subirana, 2004, Acta crystallographica. Section D, Biological crystallography.

Analysis and validation of macromolecular B values

Garib N Murshudov, G. Murshudov, Rafiga C Masmaliyeva, 2019, Acta crystallographica. Section D, Structural biology.

Recent Advances in Low Resolution Refinement Tools in REFMAC5

G. Murshudov, F. Long, R. Nicholls, 2013 .

The predictive power of data-processing statistics

Gwyndaf Evans, James M. Parkhurst, David G. Waterman, 2020, IUCrJ.

BALBES: a molecular-replacement pipeline

G. Murshudov, A. Vagin, F. Long, 2007, Acta crystallographica. Section D, Biological crystallography.

Low Resolution Refinement of Atomic Models Against Crystallographic Data.

Garib N Murshudov, Robert A Nicholls, Oleg Kovalevskiy, 2017, Methods in molecular biology.

The CCP4 suite: integrative software for macromolecular crystallography

Soon Wen Hoh, Stuart J McNicholas, P. Emsley, 2023, Acta crystallographica. Section D, Structural biology.

Low-resolution refinement tools in REFMAC5

G. Murshudov, F. Long, R. Nicholls, 2012, Acta crystallographica. Section D, Biological crystallography.

Low-resolution refinement tools in REFMAC5

G. Murshudov, F. Long, R. Nicholls, 2012 .

The Structure of the Yeast Mitochondrial Large Ribosomal Subunit

P. Emsley, S. Scheres, V. Ramakrishnan, 2014 .

Complete automation of molecular replacement

A. A. Vagin, Fei Long, G. N. Murshudov, 2006 .

Data to knowledge: how to get meaning from your result

Helen M. Berman, Wladek Minor, Torsten Schwede, 2015, IUCrJ.

Structural basis of anticancer drug recognition and amino acid transport by LAT1

G. Murshudov, Yongchan Lee, Ryuichi Ohgaki, 2023, bioRxiv.

Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB).

J. Hoch, H. Berman, J. Westbrook, 2019, Acta crystallographica. Section D, Structural biology.

Advances in automatic model building and structure completion in the context ofARP/wARP

Serge X. Cohen, W. Mooij, G. Murshudov, 2008 .

Conformation-independent structural comparison of macromolecules with ProSMART

Garib N. Murshudov, Robert A. Nicholls, Stuart McNicholas, 2014, Acta crystallographica. Section D, Biological crystallography.

A redox switch allows binding of Fe(II) and Fe(III) ions in the cyanobacterial iron-binding protein FutA from Prochlorococcus

G. Murshudov, J. Worrall, G. Evans, 2023, bioRxiv.