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List of works by Pavel V Afonine

A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry

scientific article published on 21 August 2020

A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps

scientific article published on 30 October 2018

Accurate model annotation of a near-atomic resolution cryo-EM map.

scientific article

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

scientific article

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

scientific article published on 08 April 2019

Anomalous X-ray diffraction studies of ion transport in K channels

scientific article published in Nature Communications

Automated identification of elemental ions in macromolecular crystal structures

scientific article published on 20 March 2014

Automated map sharpening by maximization of detail and connectivity.

scientific article published on 18 May 2018

Automated structure determination with phenix

Automated structure solution with the PHENIX suite

scientific article (publication date: 2008)

Automatic multiple-zone rigid-body refinement with a large convergence radius

scientific article published on 16 July 2009

Automating crystallographic structure solution and refinement of protein-ligand complexes.

scientific article published on 25 December 2013

CERES: a cryo-EM re-refinement system for continuous improvement of deposited models

scientific article published on 01 January 2021

Combining Crystallographic and Structure-Modeling Approaches in Macromolecular Crystallography

scholarly article by Thomas C. Terwilliger et al published January 2014 in Biophysical Journal

Coupling of receptor conformation and ligand orientation determine graded activity

scientific article

Cryo-EM map interpretation and protein model-building using iterative map segmentation

scientific article published on 24 October 2019

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

scientific article published on 04 February 2021

Cryo_fit: Democratization of flexible fitting for cryo-EM

scientific article published on 03 July 2019

Crystallographic model quality at a glance

scientific article published on 20 February 2009

Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard

scientific article (publication date: June 2009)

Density modification of cryo-EM maps

scientific article published on 22 September 2020

DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs.

scientific article published in February 2018

Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition

scientific article published on 24 July 2018

Evidence of functional protein dynamics from X-ray crystallographic ensembles

scientific article

FEM: feature-enhanced map.

scientific article

Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement

scientific article

From deep TLS validation to ensembles of atomic models built from elemental motions

scientific article published on 28 July 2015

From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum.

scientific article published on 31 August 2016

From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation.

scientific article published on 8 June 2018

Graphical tools for macromolecular crystallography in PHENIX

scientific article

Implementation of the riding hydrogen model in CCTBX to support the next generation of X-ray and neutron joint refinement in Phenix

scientific article published on 13 February 2020

Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement

scientific article

Improved crystallographic structures using extensive combinatorial refinement

scientific article

Improvement of cryo-EM maps by density modification

scientific article published on 17 August 2020

Including crystallographic symmetry in quantum-based refinement: Q|R#2

scientific article published on 01 January 2020

Interactive comparison and remediation of collections of macromolecular structures.

scientific article published on 13 September 2017

Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models

scientific article published on 21 April 2007

Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard

scientific article (publication date: 2008)

Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias

scientific article published on 19 April 2008

Joint X-ray and neutron refinement with phenix.refine

scientific article

Learning About Biomolecular Solvation from Water in Protein Crystals

scientific article published on 4 February 2018

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

scientific article published on 02 October 2019

Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge

scientific article published on 29 July 2018

Metrics for comparison of crystallographic maps

scientific article

Model morphing and sequence assignment after molecular replacement

scientific article published on 18 October 2013

N-{N-[2-(3,5-Difluorophenyl)acetyl]-(S)-alanyl}-(S)-phenylglycinetert-butyl ester (DAPT): an inhibitor of γ-secretase, revealing fine electronic and hydrogen-bonding features ⬇️

scientific article published on November 6, 2010

Neutron diffraction studies of a class A beta-lactamase Toho-1 E166A/R274N/R276N triple mutant

scientific article

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

scientific article published on 03 September 2018

On macromolecular refinement at subatomic resolution with interatomic scatterers

scientific article

On the application of the expected log-likelihood gain to decision making in molecular replacement.

scientific article published on 4 April 2018

On the possibility of the observation of valence electron density for individual bonds in proteins in conventional difference maps

scientific article published on 23 January 2004

On the use of logarithmic scales for analysis of diffraction data

scientific article

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

scientific article

Polder maps: improving OMIT maps by excluding bulk solvent.

scientific article published on February 2017

Portal protein functions akin to a DNA-sensor that couples genome-packaging to icosahedral capsid maturation

scientific article

Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles

scientific article

Programming new geometry restraints: parallelity of atomic groups

scientific article published on 8 July 2015

Protein structures by spallation neutron crystallography.

scientific article published on 18 April 2008

Quantum model of catalysis based on a mobile proton revealed by subatomic x-ray and neutron diffraction studies of h-aldose reductase

scientific article

Q|R: quantum-based refinement

scientific article

Real-space quantum-based refinement for cryo-EM: Q|R#3

scientific article published on 19 November 2020

Real-space refinement in PHENIX for cryo-EM and crystallography

scientific article published on 30 May 2018

Recent developments in phasing and structure refinement for macromolecular crystallography

scientific article published on 21 August 2009

Reply to 'Misreading chaperone-substrate complexes from random noise'

scholarly article by Scott Horowitz published in October 2018

Solving the scalability issue in quantum-based refinement: Q|R#1.

scientific article published on 30 November 2017

Structure and membrane remodeling activity of ESCRT-III helical polymers

scientific article

Structure of photosystem II and substrate binding at room temperature.

scientific article

TLS from fundamentals to practice

scientific article

The Phenix software for automated determination of macromolecular structures

scientific article (publication date: September 2011)

The cryo-electron microscopy structure of human transcription factor IIH.

scientific article published on 13 September 2017

The solvent component of macromolecular crystals.

scientific article published on 30 April 2015

Towards automated crystallographic structure refinement with phenix.refine

scientific article (publication date: April 2012)

Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution

scientific article published on 16 March 2012

Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling

scientific article

Visualizing chaperone-assisted protein folding.

scientific article published on 30 May 2016

What are the current limits on determination of protonation state using neutron macromolecular crystallography?

scientific article published on 13 February 2020

phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics

scientific article

phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta

scientific article

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