TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits

Conformational Changes during Pore Formation by the Perforin-Related Protein Pleurotolysin

(2015) Natalya Lukoyanova et al.   PLOS BIOLOGY

Collaborative Computational Project for Electron cryo-Microscopy

(2015) Chris Wood et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

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

(2015) Alan Brown et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Uncertainty in integrative structural modeling

(2014) Dina Schneidman-Duhovny et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Finding the right fit: chiseling structures out of cryo-electron microscopy maps

(2014) Elizabeth Villa et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structure of a mammalian ryanodine receptor

(2014) Ran Zalk et al.   NATURE

Structure of the rabbit ryanodine receptor RyR1 at near-atomic resolution

(2014) Zhen Yan et al.   NATURE

Comprehensive structural model of the mechanochemical cycle of a mitotic motor highlights molecular adaptations in the kinesin family

(2014) Adeline Goulet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An atomic model of brome mosaic virus using direct electron detection and real-space optimization

(2014) Zhao Wang et al.   Nature Communications

Ligand-induced structural changes in the cyclic nucleotide-modulated potassium channel MloK1

(2014) Julia Kowal et al.   Nature Communications

Condorcet and borda count fusion method for ligand-based virtual screening

(2014) Ali Ahmed et al.   Journal of Cheminformatics

Conserved mechanisms of microtubule-stimulated ADP release, ATP binding, and force generation in transport kinesins

(2014) Joseph Atherton et al.   eLife

On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys

(2013) Ezgi Karaca et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

The scoring of poses in protein-protein docking: current capabilities and future directions

(2013) Iain H Moal et al.   BMC BIOINFORMATICS

Consensus among multiple approaches as a reliability measure for flexible fitting into cryo-EM data

(2013) Aqeel Ahmed et al.   JOURNAL OF STRUCTURAL BIOLOGY

Computational methods for constructing protein structure models from 3D electron microscopy maps

(2013) Juan Esquivel-Rodríguez et al.   JOURNAL OF STRUCTURAL BIOLOGY

iMODFIT: Efficient and robust flexible fitting based on vibrational analysis in internal coordinates

(2013) José Ramón Lopéz-Blanco et al.   JOURNAL OF STRUCTURAL BIOLOGY

Combined approaches to flexible fitting and assessment in virus capsids undergoing conformational change

(2013) Arun Prasad Pandurangan et al.   JOURNAL OF STRUCTURAL BIOLOGY

Cryo-EM model validation using independent map reconstructions

(2013) Frank DiMaio et al.   PROTEIN SCIENCE

Integrative Structural Biology

(2013) A. B. Ward et al.   SCIENCE

Conformational States of Macromolecular Assemblies Explored by Integrative Structure Calculation

(2013) Konstantinos Thalassinos et al.   STRUCTURE

Recommendations of the wwPDB NMR Validation Task Force

(2013) Gaetano T. Montelione et al.   STRUCTURE

A Family of Algorithms for Computing Consensus about Node State from Network Data

(2013) Eleanor R. Brush et al.   PLoS Computational Biology

The 2010 cryo-em modeling challenge

(2012) Steven J. Ludtke et al.   BIOPOLYMERS

Structure of the Rigor Actin-Tropomyosin-Myosin Complex

(2012) Elmar Behrmann et al.   CELL

Go hybrid: EM, crystallography, and beyond

(2012) Gabriel C Lander et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Cryo-electron microscopy - a primer for the non-microscopist

(2012) Jacqueline L. S. Milne et al.   FEBS Journal

Fitting Multimeric Protein Complexes into Electron Microscopy Maps Using 3D Zernike Descriptors

(2012) Juan Esquivel-Rodríguez et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Outcome of the First Electron Microscopy Validation Task Force Meeting

(2012) Richard Henderson et al.   STRUCTURE

Scoring functions for cryoEM density fitting

(2011) Daven Vasishtan et al.   JOURNAL OF STRUCTURAL BIOLOGY

Consensus among flexible fitting approaches improves the interpretation of cryo-EM data

(2011) Aqeel Ahmed et al.   JOURNAL OF STRUCTURAL BIOLOGY

Finding rigid bodies in protein structures: Application to flexible fitting into cryoEM maps

(2011) Arun Prasad Pandurangan et al.   JOURNAL OF STRUCTURAL BIOLOGY

The amino-terminal disease hotspot of ryanodine receptors forms a cytoplasmic vestibule

(2010) Ching-Chieh Tung et al.   NATURE

Super-resolution biomolecular crystallography with low-resolution data

(2010) Gunnar F. Schröder et al.   NATURE

Direct visualization of secondary structures of F-actin by electron cryomicroscopy

(2010) Takashi Fujii et al.   NATURE

Dali server: conservation mapping in 3D

(2010) Liisa Holm et al.   NUCLEIC ACIDS RESEARCH

Determining macromolecular assembly structures by molecular docking and fitting into an electron density map

(2010) Keren Lasker et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Confidence intervals for fitting of atomic models into low-resolution densities

(2009) Niels Volkmann   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Biased coarse-grained molecular dynamics simulation approach for flexible fitting of X-ray structure into cryo electron microscopy maps

(2009) Ivan Grubisic et al.   JOURNAL OF STRUCTURAL BIOLOGY

Comprehensive Molecular Structure of the Eukaryotic Ribosome

(2009) Derek J. Taylor et al.   STRUCTURE

Integrating Diverse Data for Structure Determination of Macromolecular Assemblies

(2008) Frank Alber et al.   Annual Review of Biochemistry

A detailed analysis of 3D subcellular signal localization

(2008) Amalka Pinidiyaarachchi et al.   CYTOMETRY PART A

A method for the alignment of heterogeneous macromolecules from electron microscopy

(2008) Maxim Shatsky et al.   JOURNAL OF STRUCTURAL BIOLOGY

Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel

(2008) I. I. Serysheva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein Structure Fitting and Refinement Guided by Cryo-EM Density

(2008) Maya Topf et al.   STRUCTURE

Structure of the Mammalian 80S Ribosome at 8.7 Å Resolution

(2008) Preethi Chandramouli et al.   STRUCTURE

Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics

(2008) Leonardo G. Trabuco et al.   STRUCTURE

Crystallographic Conformers of Actin in a Biologically Active Bundle of Filaments

(2007) Yao Cong et al.   JOURNAL OF MOLECULAR BIOLOGY