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biochemistry & molecular biology (46) 46
biophysics (41) 41
real-space refinement (41) 41
models, molecular (39) 39
crystallography (35) 35
index medicus (35) 35
biochemical research methods (28) 28
cryoelectron microscopy (22) 22
protein conformation (20) 20
refinement (19) 19
analysis (17) 17
electron microscopy (17) 17
resolution (17) 17
cell biology (16) 16
crystallography, x-ray (16) 16
crystal-structure (14) 14
crystal-structures (14) 14
crystals (14) 14
cryo-em (13) 13
cryoelectron microscopy - methods (13) 13
maps (13) 13
article (12) 12
proteins - chemistry (12) 12
proteins (11) 11
software (11) 11
crystal structure (10) 10
crystallography, x-ray - methods (10) 10
density (10) 10
electrons (10) 10
angstrom resolution (9) 9
electron-density maps (9) 9
models (9) 9
molecular-dynamics (9) 9
multidisciplinary sciences (9) 9
protein structures (9) 9
real‐space refinement (9) 9
algorithms (8) 8
macromolecular structures (8) 8
microscopy (8) 8
model (8) 8
molecular structure (8) 8
real-space observation (8) 8
research papers (8) 8
validation (8) 8
computer simulation (7) 7
diffraction (7) 7
electron density (7) 7
humans (7) 7
nucleic acid conformation (7) 7
protein structure, tertiary (7) 7
structure (7) 7
x-ray crystallography (7) 7
atomic models (6) 6
atomic structures (6) 6
complex (6) 6
condensed matter physics, superconductivity and superfluidity (6) 6
databases, protein (6) 6
macromolecular substances - chemistry (6) 6
mathematical models (6) 6
methods (6) 6
molecular dynamics (6) 6
protein structure, secondary (6) 6
research (6) 6
70s ribosome (5) 5
atoms (5) 5
biological sciences (5) 5
cryo-electron microscopy (5) 5
electron-microscopy (5) 5
errors (5) 5
flexible fitting (5) 5
low-resolution (5) 5
maximum-likelihood (5) 5
molecular dynamics simulation (5) 5
molecular sequence data (5) 5
phenix (5) 5
physics, condensed matter (5) 5
protein (5) 5
real-space (5) 5
real-space envelopes (5) 5
ribosome (5) 5
ribosomes - chemistry (5) 5
rna (5) 5
structural biology (5) 5
transfer rna (5) 5
3-dimensional structure (4) 4
amino acid sequence (4) 4
animals (4) 4
biology (4) 4
chemical properties (4) 4
condensed matter - materials science (4) 4
cryo-em density (4) 4
crystallographic refinement (4) 4
free r-value (4) 4
macromolecular substances (4) 4
messenger rna (4) 4
microscopy maps (4) 4
microscopy, electron (4) 4
model building (4) 4
molecular biology (4) 4
optimization (4) 4
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1. Full Text Towards automated crystallographic structure refinement with phenix.refine
by Afonine, Pavel V and Grosse‐Kunstleve, Ralf W and Echols, Nathaniel and Headd, Jeffrey J and Moriarty, Nigel W and Mustyakimov, Marat and Terwilliger, Thomas C and Urzhumtsev, Alexandre and Zwart, Peter H and Adams, Paul D
Acta Crystallographica Section D, ISSN 0907-4449, 04/2012, Volume 68, Issue 4, pp. 352 - 367
phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper... 
real‐space refinement | twinning | structure refinement | simulated annealing | joint X‐ray/neutron refinement | maximum likelihood | PHENIX | TLS | subatomic resolution | NCS | real-space refinement | NCS Model building, refinement and validation | joint X-ray/neutron refinement | MACROMOLECULAR REFINEMENT | REAL-SPACE REFINEMENT | CRYSTAL-STRUCTURE | PROTEIN-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | BIOCHEMICAL RESEARCH METHODS | ELECTRON-DENSITY MAPS | X-RAY-DIFFRACTION | CRYSTALLOGRAPHY | BIOPHYSICS | STRUCTURE VALIDATION | DATA-BANK | FREE R-VALUE | THERMAL-MOTION | Crystallography, X-Ray - methods | Models, Molecular | Software | Automation | Twinning (Crystallography) | Mechanization | Particle accelerators | Mineralogy | Diffraction | Parametrization | Automated | Neutron diffraction | Packages | Strategy | Deposition | Readers | Crystal structure | NEUTRONS | DEPOSITION | RESOLUTION | CRYSTALS | INTERFACES | VALIDATION | CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY | EXPERIMENTAL DATA | NEUTRON DIFFRACTION | TWINNING
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2. Full Text Real‐space refinement in PHENIX for cryo‐EM and crystallography
by Afonine, Pavel V and Poon, Billy K and Read, Randy J and Sobolev, Oleg V and Terwilliger, Thomas C and Urzhumtsev, Alexandre and Adams, Paul D and Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States) and Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Acta Crystallographica Section D, ISSN 2059-7983, 06/2018, Volume 74, Issue 6, pp. 531 - 544
This article describes the implementation of real‐space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified... 
real‐space refinement | crystallography | PHENIX | atomic‐centered targets | cryo‐EM | map interpolation | Atomic-centered targets | Real-space refinement | Map interpolation | Crystallography | Cryo-EM | SYSTEM | VISUALIZATION | PHASES | BIOCHEMISTRY & MOLECULAR BIOLOGY | BIOCHEMICAL RESEARCH METHODS | VALIDATION | MICROSCOPY DATA | MODEL | ATOMIC-RESOLUTION | SOFTWARE | real-space refinement | ANGSTROM RESOLUTION | BIOPHYSICS | atomic-centered targets | cryo-EM | TOOLS | Animals | Macromolecular Substances - chemistry | Validation Studies as Topic | Computer Simulation | Humans | Crystallography - methods | Models, Molecular | TRPV Cation Channels - chemistry | Software | Cryoelectron Microscopy - methods | Databases, Protein - standards | Proteins | Molecular modelling | Constraints | Data banks | Maps | Atomic structure | Molecular chains | BASIC BIOLOGICAL SCIENCES | Biological Science | MATHEMATICS AND COMPUTING
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3. Full Text Tools for macromolecular model building and refinement into electron cryo‐microscopy reconstructions
by Brown, Alan and Long, Fei and Nicholls, Robert A and Toots, Jaan and Emsley, Paul and Murshudov, Garib
Acta Crystallographica Section D, ISSN 1399-0047, 01/2015, Volume 71, Issue 1, pp. 136 - 153
The recent rapid development of single‐particle electron cryo‐microscopy (cryo‐EM) now allows structures to be solved by this method at resolutions close to 3... 
LIBG | model building | refinement | electron cryo‐microscopy reconstructions | LIBG Crystallography and complementary methods | electron cryo-microscopy reconstructions | REAL-SPACE REFINEMENT | MICROSCOPY MAPS | RESOLUTION DENSITY MAPS | BIOCHEMISTRY & MOLECULAR BIOLOGY | BIOCHEMICAL RESEARCH METHODS | EM STRUCTURE DETERMINATION | CRYO-EM | CRYSTAL-STRUCTURES | CRYSTALLOGRAPHY | 26S PROTEASOME | MOLECULAR-REPLACEMENT | BIOPHYSICS | CROSS-VALIDATION | Models, Molecular | Crystallography, X-Ray | Macromolecular Substances - chemistry | Cryoelectron Microscopy - methods | Microscope and microscopy | DENSITY | MODIFICATIONS | ELECTRONS | RESOLUTION | CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY | ATOMS | RELIABILITY | MICROSCOPY | INTERATOMIC DISTANCES
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4. Full Text Atomic modeling of cryo-electron microscopy reconstructions – Joint refinement of model and imaging parameters
by Chapman, Brynmor K and Chapman, Michael S and Trzynka, Andrew
Journal of Structural Biology, ISSN 1047-8477, 04/2013, Volume 182, Issue 1, pp. 10 - 21
When refining the fit of component atomic structures into electron microscopic reconstructions, use of a resolution-dependent atomic density function makes it... 
B-factor | Fitting | Restraint | Structure | Flexibility | Optimization | Resolution | SYSTEM | REAL-SPACE REFINEMENT | MOLECULAR-DYNAMICS | DENSITY MAPS | BIOCHEMISTRY & MOLECULAR BIOLOGY | ALGORITHM | CRYO-EM | TRANSDUCTION | VECTOR | CELL BIOLOGY | BIOPHYSICS | CRYSTALLOGRAPHIC REFINEMENT | Immunoglobulin Fab Fragments - ultrastructure | Protein Structure, Tertiary | Archaeal Proteins - chemistry | Chaperonins - chemistry | Methanococcus - chemistry | Models, Molecular | Chaperonins - ultrastructure | Fourier Analysis | Image Processing, Computer-Assisted | Dependovirus - ultrastructure | Immunoglobulin Fab Fragments - chemistry | Archaeal Proteins - ultrastructure | Cryoelectron Microscopy - methods | Monoclonal antibodies | Models | Electron microscopy | Crystals
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5. Full Text Real‐space refinement with DireX: From global fitting to side‐chain improvements
by Wang, Zhe and Schröder, Gunnar F
Biopolymers, ISSN 0006-3525, 09/2012, Volume 97, Issue 9, pp. 687 - 697
Single‐particle cryo‐electron microscopy (cryo‐EM) has become an important tool to determine the structure of large biomolecules and assemblies thereof.... 
real‐space refinement | low resolution | flexible fitting | Cryo‐EM | DireX | real-space refinement | Cryo-EM | MOLECULAR-DYNAMICS | X-RAY CRYSTALLOGRAPHY | CRYOELECTRON MICROSCOPY | BIOCHEMISTRY & MOLECULAR BIOLOGY | ELECTRON-MICROSCOPY MAPS | CRYSTAL-STRUCTURES | GROUP-II CHAPERONIN | CRYO-EM DENSITY | BIOPHYSICS | RESOLUTION PROTEIN STRUCTURES | ATOMIC STRUCTURES | SECONDARY STRUCTURE | Chaperonin 60 - chemistry | Aquaporins - chemistry | Capsid Proteins - chemistry | Eye Proteins - chemistry | Models, Molecular | Antigens, Viral - chemistry | Chaperonin 10 - chemistry | Software | Proteins - chemistry | Cryoelectron Microscopy - methods
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6. Full Text New model‐fitting and model‐completion programs for automated iterative nucleic acid refinement
by Yamashita, Keitaro and Zhou, Yong and Tanaka, Isao and Yao, Min
Acta Crystallographica Section D, ISSN 0907-4449, 06/2013, Volume 69, Issue 6, pp. 1171 - 1179
In the past decade many structures of nucleic acids have been determined, which have contributed to our understanding of their biological functions. However,... 
real‐space refinement | automatic refinement | nucleic acid model fitting | nucleic acid model building | LAFIRE | real-space refinement | SYSTEM | CRYSTAL-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | BIOCHEMICAL RESEARCH METHODS | MOLPROBITY | CRYSTALLOGRAPHY | PHENIX | SOFTWARE | BIOPHYSICS | STRUCTURE VALIDATION | TRANSFER-RNA | ATOMIC-ACCURACY | BINDING | Crystallography, X-Ray - methods | Models, Molecular | Software | Nucleic Acids - chemistry | Molecular Conformation | Nucleic acids | Universities and colleges | Ribonucleic acid--RNA | Automation | Deoxyribonucleic acid--DNA
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7. Full Text 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
by Brunger, Axel T and Das, Debanu and Deacon, Ashley M and Grant, Joanna and Terwilliger, Thomas C and Read, Randy J and Adams, Paul D and Levitt, Michael and Schröder, Gunnar F
Acta Crystallographica Section D, ISSN 0907-4449, 04/2012, Volume 68, Issue 4, pp. 391 - 403
Phasing by molecular replacement remains difficult for targets that are far from the search model or in situations where the crystal diffracts only weakly or... 
real‐space refinement | reciprocal‐space refinement | DEN refinement | succinyl‐diaminopimelate desuccinylase | automated model building | reciprocal-space refinement | real-space refinement | succinyl-diaminopimelate desuccinylase Model building, refinement and validation | SYSTEM | PROTEIN | BIOCHEMISTRY & MOLECULAR BIOLOGY | BIOCHEMICAL RESEARCH METHODS | VALIDATION | CRYSTALLOGRAPHY | SOFTWARE | DENSITY | BIOPHYSICS | ALIGNMENT | IMPROVEMENT | CRYSTALS | DIFFRACTION | Crystallography, X-Ray - methods | Amino Acid Sequence | Sequence Alignment | Models, Molecular | Molecular Sequence Data | Corynebacterium glutamicum - enzymology | Software | Structural Homology, Protein | Amidohydrolases - analysis | Amidohydrolases - chemistry | Automation, Laboratory - methods | Nuclear radiation | Models | Particle accelerators | Automation | Catalysis | Research Papers | succinyl-diaminopimelate desuccinylase
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8. Full Text Application of constrained real‐space refinement of flexible molecular fragments to automatic model building of RNA structures
by Pavelcik, Frantisek
Journal of Applied Crystallography, ISSN 0021-8898, 04/2012, Volume 45, Issue 2, pp. 309 - 315
New methods have been developed for locating phosphate groups and nucleic acid bases in the electron density of RNA structures. These methods utilize a... 
real‐space refinement | rotation function | computer programs | nucleic acid model building | X‐ray crystallography | molecular fragments | translation function | electron density interpretation | X-ray crystallography | real-space refinement | ANGSTROM RESOLUTION | TRANSLATION FUNCTION | MACROMOLECULAR STRUCTURES | CRYSTAL-STRUCTURE | TORSION-ANGLE SPACE | PHASED ROTATION | CRYSTALLOGRAPHY | PROTEIN DATA-BANK | MAP INTERPRETATION | CONFORMATION | ELECTRON-DENSITY | Phosphates | RNA | Nucleic acids | Ribonucleic acid--RNA | Crystallography | Crystal structure | Electrons
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9. Full Text Building and Refining Protein Models within Cryo-electron Microscopy Density Maps Based on Homology Modeling and Multiscale Structure Refinement
by Zhu, Jiang and Cheng, Lingpeng and Fang, Qin and Zhou, Z. Hong and Honig, Barry
Journal of Molecular Biology, ISSN 0022-2836, 04/2010, Volume 397, Issue 3, pp. 835 - 851
Automatic modeling methods using cryoelectron microscopy (cryoEM) density maps as constraints are promising approaches to building atomic models of individual... 
structure refinement | density fitting | homology modeling | protein structure prediction | cryo-electron microscopy | LOW-RESOLUTION | REAL-SPACE REFINEMENT | MACROMOLECULAR STRUCTURES | MOLECULAR-DYNAMICS | BIOCHEMISTRY & MOLECULAR BIOLOGY | ELECTRON-MICROSCOPY | SEQUENCE PROFILES | CRYOEM DENSITY | REOVIRUS CORE | ATOMIC MODELS | FOLD RECOGNITION | Cryoelectron Microscopy | Protein Structure, Tertiary | Sequence Homology, Amino Acid | Amino Acid Sequence | Computational Biology | Models, Molecular | Molecular Sequence Data | Protein Conformation | Software | Proteins - chemistry | Molecular Dynamics Simulation | Viral proteins | Electron microscopy | Analysis
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10. Full Text Low-resolution structure refinement in electron microscopy
by Chen, James Z and Fürst, Johannes and Chapman, Michael S and Grigorieff, Nikolaus
Journal of Structural Biology, ISSN 1047-8477, 2003, Volume 144, Issue 1, pp. 144 - 151
A real-space structure refinement method, originally developed for macromolecular X-ray crystallography, has been applied to protein structure analysis by... 
Macromolecular structure | Electron microscopy | Empirical force field | Electron density map | Real-space structure refinement | REAL-SPACE REFINEMENT | MOLECULAR-DYNAMICS | DOMAIN | SENSITIVE FACTOR | empirical force field | BIOCHEMISTRY & MOLECULAR BIOLOGY | CRYSTAL-STRUCTURES | RECEPTOR | electron density map | CELL BIOLOGY | real-space structure refinement | ANGSTROM RESOLUTION | BIOPHYSICS | electron microscopy | BACTERIORHODOPSIN | macromolecular structure | RIBOSOME | Protein Structure, Tertiary | Biophysical Phenomena | Protein Structure, Secondary | Bacterial Proteins - chemistry | Models, Molecular | Biophysics | Blood Proteins - chemistry | N-Ethylmaleimide-Sensitive Proteins | Protein Folding | Crystallography, X-Ray - methods | Microscopy, Electron - methods | Actins - chemistry | Carrier Proteins - chemistry | Ligands | Protein Conformation | Electrons | Vesicular Transport Proteins
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11. Full Text BCL::EM-Fit: Rigid body fitting of atomic structures into density maps using geometric hashing and real space refinement
by Woetzel, Nils and Lindert, Steffen and Stewart, Phoebe L and Meiler, Jens
Journal of Structural Biology, ISSN 1047-8477, 09/2011, Volume 175, Issue 3, pp. 264 - 276
Cryo-electron microscopy (cryoEM) can visualize large macromolecular assemblies at resolutions often below 10 Å and recently as good as 3.8–4.5 Å. These... 
Monte Carlo Metropolis | Fitting | Geometric hashing | Real space | Docking | Cryo-electron microscopy | CryoEM | LOW-RESOLUTION | CRYOELECTRON MICROSCOPY | BIOCHEMISTRY & MOLECULAR BIOLOGY | SITUS | ELECTRON-MICROSCOPY | CRYO-EM | MODEL | CELL BIOLOGY | VARIABILITY | PROTEIN STRUCTURES | BIOPHYSICS | Adenoviridae - ultrastructure | Algorithms | Cryoelectron Microscopy - methods | Monte Carlo Method | Physiological aspects | Viral proteins | Structure | Analysis | Crystals | docking | cryoEM | geometric hashing | fitting | real space
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12. Full Text Analysis of Structural Dynamics in the Ribosome by TLS Crystallographic Refinement
by Korostelev, Andrei and Noller, Harry F
Journal of Molecular Biology, ISSN 0022-2836, 2007, Volume 373, Issue 4, pp. 1058 - 1070
A major goal in the study of ribosome structure and function is to obtain a complete description of the conformational dynamics of the ribosome during the many... 
X-ray crystallography | TLS refinement | structural dynamics | 70 S ribosome | SEGMENTED ANISOTROPIC REFINEMENT | REAL-SPACE REFINEMENT | TRANSFER-RNA COMPLEX | CRYOELECTRON MICROSCOPY | CRYSTAL-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | ELONGATION-FACTOR G | ANGSTROM RESOLUTION | MESSENGER-RNA | COLI 70S RIBOSOME | INTERSUBUNIT MOVEMENT | Crystallography, X-Ray - methods | Protein Structure, Tertiary | Protein Structure, Secondary | Ribosome Subunits, Large, Bacterial - chemistry | Ribosomes - chemistry | Models, Molecular | Ribosome Subunits, Small, Bacterial - chemistry | RNA | Protein biosynthesis | Analysis
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13. Full Text Crystallographic structure refinement in a nutshell
by Afonine, Pavel V and Adams, Paul D
NATO Science for Peace and Security Series A: Chemistry and Biology, ISSN 1874-6489, 2013, pp. 211 - 219
Crystallographic structure refinement | Maximum-likelihood | TLS | Twinning | Real-space | ADP
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14. Full Text ISOLDE: a physically realistic environment for model building into low‐resolution electron‐density maps
by Croll, Tristan Ian
Acta Crystallographica Section D, ISSN 2059-7983, 06/2018, Volume 74, Issue 6, pp. 519 - 530
This paper introduces ISOLDE , a new software package designed to provide an intuitive environment for high‐fidelity interactive remodelling/refinement of... 
real‐space refinement | ISOLDE | visualization | model building | molecular dynamics | Molecular dynamics | Visualization | Model building | Real-space refinement | ERRORS | STRUCTURE REFINEMENT | BIOCHEMISTRY & MOLECULAR BIOLOGY | BIOCHEMICAL RESEARCH METHODS | VALIDATION | CRYSTALLOGRAPHY | PHENIX | PARAMETERS | real-space refinement | BIOPHYSICS | DYNAMICS | GENERATION | TOOLS | Fungal Proteins - chemistry | Macromolecular Substances - chemistry | Validation Studies as Topic | Data Accuracy | Computer Simulation | Models, Molecular | Software | Cryoelectron Microscopy - methods | Minichromosome Maintenance Proteins - chemistry | Molecular Dynamics Simulation | DNA helicase | Animal models | Molecular modelling | Maps | Macromolecules | Computer graphics | Tactile stimuli | Molecular chains
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15. Full Text Protein Structure Fitting and Refinement Guided by cryoEM Density
by Topf, Maya and Lasker, Keren and Webb, Ben and Wolfson, Haim and Chiu, Wah and Sali, Andrej
Structure (London, England : 1993), ISSN 0969-2126, 2/2008, Volume 16, Issue 2, pp. 295 - 307
For many macromolecular assemblies, both a cryoEM map and atomic structures of its component proteins are available. Here, we describe a method for fitting and... 
real-space refinement | density fitting | comparative modeling | flexible fitting | protein structure prediction | cryo-EM | cryo-electron microscopy
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