Cryo‐electron microscopy targets in CASP13: Overview and evaluation of results

A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments

(2019) Luciano A. Abriata et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

CASP13 target classification into tertiary structure prediction categories

(2019) Lisa N. Kinch et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of protein assembly prediction in CASP13

(2019) Dmytro Guzenko et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Evaluation of template‐based modeling in CASP13

(2019) Tristan I. Croll et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment

(2019) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Evaluation system and web infrastructure for the second cryo-EM model challenge

(2018) Andriy Kryshtafovych et al.   JOURNAL OF STRUCTURAL BIOLOGY

Comparative analysis of methods for evaluation of protein models against native structures

(2018) Kliment Olechnovič et al.   BIOINFORMATICS

New tools for the analysis and validation of cryo-EM maps and atomic models

(2018) Pavel V. Afonine et al.   Acta Crystallographica Section D-Structural Biology

Comparing cryo-EM structures

(2018) Catherine L. Lawson et al.   JOURNAL OF STRUCTURAL BIOLOGY

Assessment of protein assembly prediction in CASP12

(2017) Aleix Lafita et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of hard target modeling in CASP12 reveals an emerging role of alignment-based contact prediction methods

(2017) Luciano A. Abriata et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Evaluation of the template-based modeling in CASP12

(2017) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology

(2017) Martino Bertoni et al.   Scientific Reports

De Novo modeling in cryo-EM density maps with Pathwalking

(2016) Muyuan Chen et al.   JOURNAL OF STRUCTURAL BIOLOGY

Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment

(2016) Agnel Praveen Joseph et al.   METHODS

EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy

(2015) Benjamin A Barad et al.   NATURE METHODS

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

(2015) Irene Farabella et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests

(2013) Valerio Mariani et al.   BIOINFORMATICS

CAD-score: A new contact area difference-based function for evaluation of protein structural models

(2013) Kliment Olechnovič et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL

(2013) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

An automatic method for CASP9 free modeling structure prediction assessment

(2011) Qian Cong et al.   BIOINFORMATICS

Scoring functions for cryoEM density fitting

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

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Protein Structure Fitting and Refinement Guided by Cryo-EM Density

(2008) Maya Topf et al.   STRUCTURE