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science & technology (45) 45
physical sciences (29) 29
crystallography (28) 28
biochemistry & molecular biology (26) 26
life sciences & biomedicine (26) 26
biophysics (22) 22
models, molecular (22) 22
biochemical research methods (15) 15
real-space refinement (15) 15
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chemistry, multidisciplinary (8) 8
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proteins (8) 8
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crystallography, x-ray (6) 6
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molecular structure (5) 5
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cryoelectron microscopy (4) 4
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mathematical analysis (4) 4
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protein structure, secondary (4) 4
real-space methods (4) 4
research (4) 4
ribonucleic acid--rna (4) 4
science & technology - other topics (4) 4
structure (4) 4
validation (4) 4
animals (3) 3
capsid proteins - chemistry (3) 3
computer science (3) 3
condensed matter: structure, mechanical and thermal properties (3) 3
cryo‐em (3) 3
databases, protein (3) 3
density functional theory (3) 3
flexible fitting (3) 3
humans (3) 3
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nucleic acid conformation (3) 3
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structure of solids and liquids; crystallography (3) 3
technology (3) 3
tls (3) 3
transfer rna (3) 3
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x-ray crystallography (3) 3
accuracy (2) 2
adp (2) 2
amino acid sequence (2) 2
arginine kinase - chemistry (2) 2
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automatic model building (2) 2
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biologi (2) 2
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condensed matter physics, superconductivity and superfluidity (2) 2
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correlations (2) 2
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1. 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, Structural biology, ISSN 2059-7983, 06/2018, Volume 74, Issue 6, pp. 531 - 544
real‐space refinement | crystallography | PHENIX | atomic‐centered targets | cryo‐EM | map interpolation | Atomic-centered targets | Real-space refinement | Map interpolation | Crystallography | Cryo-EM | 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 | Index Medicus | BASIC BIOLOGICAL SCIENCES | Biological Science | MATHEMATICS AND COMPUTING
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2. 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, Biological crystallography., ISSN 1399-0047, 04/2012, Volume 68, Issue 4, pp. 352 - 367
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 | Biochemistry & Molecular Biology | Physical Sciences | Life Sciences & Biomedicine | Biochemical Research Methods | Biophysics | Crystallography | Science & Technology | Crystallography, X-Ray - methods | Models, Molecular | Software | Automation | Twinning (Crystallography) | Mechanization | Particle accelerators | Mineralogy | Diffraction | Index Medicus | 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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3. 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
real‐space refinement | low resolution | flexible fitting | Cryo‐EM | DireX | real-space refinement | Cryo-EM | Biochemistry & Molecular Biology | Biophysics | Life Sciences & Biomedicine | Science & Technology | 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 | Index Medicus
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4. Full Text Data-guided Multi-Map variables for ensemble refinement of molecular movies
by Vant, John W and Sarkar, Daipayan and Streitwieser, Ellen and Fiorin, Giacomo and Skeel, Robert and Vermaas, Josh V and Singharoy, Abhishek and Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)
The Journal of chemical physics, ISSN 0021-9606, 12/2020, Volume 153, Issue 21, pp. 214102 - 214102
Physical Sciences | Chemistry | Physics, Atomic, Molecular & Chemical | Chemistry, Physical | Physics | Science & Technology | Proteins | Simulation | Molecular dynamics | Energy costs | Electron density | Crystallography | Free energy | Index Medicus | steered molecular dynamics | x-ray crystallography | potential energy surfaces | INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY | covariance and correlation | real-space methods | free energy | proteins | molecular dynamics | cryogenic electron microscopy
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5. Full Text Real‐space quantum‐based refinement for cryo‐EM: Q|R#3
by Wang, Lum and Kruse, Holger and Sobolev, Oleg V and Moriarty, Nigel W and Waller, Mark P and Afonine, Pavel V and Biczysko, Malgorzata
Acta crystallographica. Section D, Structural biology, ISSN 2059-7983, 12/2020, Volume 76, Issue 12, pp. 1184 - 1191
quantum refinement | real‐space refinement | crystallography | cryo‐EM | protein | phenix.comparama | real-space refinement | cryo-EM | Biochemistry & Molecular Biology | Physical Sciences | Life Sciences & Biomedicine | Biochemical Research Methods | Biophysics | Crystallography | Science & Technology | Chains | Algorithms | Maps | Index Medicus
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6. 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 1600-5767, 04/2012, Volume 45, Issue 2, pp. 309 - 315
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 | Physical Sciences | Chemistry | Chemistry, Multidisciplinary | Crystallography | Science & Technology | Phosphates | RNA | Nucleic acids | Ribonucleic acid--RNA | Crystal structure | Electrons
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7. 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
Macromolecular structure | Electron microscopy | Empirical force field | Electron density map | Real-space structure refinement | Biochemistry & Molecular Biology | Biophysics | Life Sciences & Biomedicine | Science & Technology | Cell Biology | Protein Structure, Tertiary | Biophysical Phenomena | Protein Structure, Secondary | Bacterial Proteins - chemistry | Models, Molecular | 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 | Index Medicus
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8. 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
Monte Carlo Metropolis | Fitting | Geometric hashing | Real space | Docking | Cryo-electron microscopy | CryoEM | Biochemistry & Molecular Biology | Biophysics | Life Sciences & Biomedicine | Science & Technology | Cell Biology | Adenoviridae - ultrastructure | Algorithms | Cryoelectron Microscopy - methods | Monte Carlo Method | Physiological aspects | Viral proteins | Structure | Analysis | Crystals | Index Medicus | docking | cryoEM | geometric hashing | fitting | real space
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9. Full Text Current developments in Coot for macromolecular model building of Electron Cryo‐microscopy and Crystallographic Data
by Casañal, Ana and Lohkamp, Bernhard and Emsley, Paul
Protein science, ISSN 0961-8368, 04/2020, Volume 29, Issue 4, pp. 1069 - 1078
ligands | real space refinement | molecular biophysics | rotamers | macromolecular model building | validation | Life Sciences & Biomedicine | Biochemistry & Molecular Biology | Science & Technology | Constraints | Maps | Molecular structure | Buildings | Macromolecules | Morphing | Crystallography | Index Medicus | Tools for Protein Science | Medicin och hälsovetenskap
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10. 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, Biological crystallography., ISSN 1399-0047, 06/2013, Volume 69, Issue 6, pp. 1171 - 1179
real‐space refinement | automatic refinement | nucleic acid model fitting | nucleic acid model building | LAFIRE | real-space refinement | Biochemistry & Molecular Biology | Physical Sciences | Life Sciences & Biomedicine | Biochemical Research Methods | Biophysics | Crystallography | Science & Technology | Crystallography, X-Ray - methods | Models, Molecular | Software | Nucleic Acids - chemistry | Molecular Conformation | Nucleic acids | Universities and colleges | Ribonucleic acid--RNA | Automation | Deoxyribonucleic acid--DNA | Index Medicus
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