Lista de obras -

A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry

artículo científico publicado en 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.

artículo científico publicado en 2017

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

artículo científico publicado en 2014

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

artículo científico publicado en 2018

Automated identification of elemental ions in macromolecular crystal structures

artículo científico publicado en 2014

Automated map sharpening by maximization of detail and connectivity.

artículo científico publicado en 2018

Automated structure determination with phenix

Automated structure solution with the PHENIX suite

artículo científico publicado en 2008

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

artículo científico publicado en 2009

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

artículo científico publicado en 2013

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

artículo científico publicado en 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

artículo científico publicado en 2010

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

artículo científico publicado en 2021

Cryo_fit: Democratization of flexible fitting for cryo-EM

scientific article published on 03 July 2019

Crystallographic model quality at a glance

artículo científico publicado en 2009

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

artículo científico publicado en 2009

Density modification of cryo-EM maps

artículo científico publicado en 2020

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

artículo científico publicado en 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

artículo científico publicado en 2010

FEM: feature-enhanced map.

artículo científico publicado en 2015

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

artículo científico publicado en 2014

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

artículo científico publicado en 2015

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

artículo científico publicado en 2016

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

artículo científico publicado en 2018

Graphical tools for macromolecular crystallography in PHENIX

artículo científico publicado en 2012

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

artículo científico publicado en 2020

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

artículo científico publicado en 2012

Improved crystallographic structures using extensive combinatorial refinement

artículo científico publicado en 2013

Improvement of cryo-EM maps by density modification

artículo científico publicado en 2020

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

artículo científico publicado en 2020

Interactive comparison and remediation of collections of macromolecular structures.

artículo científico publicado en 2017

Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models

artículo científico publicado en 2007

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

artículo científico publicado en 2008

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

artículo científico publicado en 2008

Joint X-ray and neutron refinement with phenix.refine

artículo científico publicado en 2010

Learning About Biomolecular Solvation from Water in Protein Crystals

artículo científico publicado en 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

artículo científico publicado en 2014

Model morphing and sequence assignment after molecular replacement

artículo científico publicado en 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 ⬇️

artículo científico publicado el 6 de noviembre de 2010

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

artículo científico publicado en 2010

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

artículo científico publicado en 2018

On macromolecular refinement at subatomic resolution with interatomic scatterers

artículo científico publicado en 2007

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

artículo científico publicado en 2018

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

artículo científico publicado en 2004

On the use of logarithmic scales for analysis of diffraction data

artículo científico publicado en 2009

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

artículo científico publicado en 2010

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

artículo científico publicado en 2017

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

artículo científico publicado en 2015

Programming new geometry restraints: parallelity of atomic groups

artículo científico publicado en 2015

Protein structures by spallation neutron crystallography.

artículo científico publicado en 2008

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

artículo científico publicado en 2008

Q|R: quantum-based refinement

artículo científico publicado en 2017

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

artículo científico publicado en 2020

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

artículo científico publicado en 2018

Recent developments in phasing and structure refinement for macromolecular crystallography

artículo científico publicado en 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.

artículo científico publicado en 2017

Structure and membrane remodeling activity of ESCRT-III helical polymers

artículo científico publicado en 2015

Structure of photosystem II and substrate binding at room temperature.

artículo científico publicado en 2016

TLS from fundamentals to practice

artículo científico publicado en 2013

The Phenix software for automated determination of macromolecular structures

artículo científico publicado en 2011

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

artículo científico publicado en 2017

The solvent component of macromolecular crystals.

artículo científico publicado en 2015

Towards automated crystallographic structure refinement with phenix.refine

artículo científico publicado en 2012

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

artículo científico publicado en 2012

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

artículo científico publicado en 2013

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?

artículo científico publicado en 2020

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

artículo científico publicado en 2010

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

artículo científico publicado en 2012

Lista de obras de

A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry

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

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

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

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

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

Automated identification of elemental ions in macromolecular crystal structures

Automated map sharpening by maximization of detail and connectivity.

Automated structure determination with phenix

Automated structure solution with the PHENIX suite

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

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

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

Combining Crystallographic and Structure-Modeling Approaches in Macromolecular Crystallography

Coupling of receptor conformation and ligand orientation determine graded activity

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

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

Cryo_fit: Democratization of flexible fitting for cryo-EM

Crystallographic model quality at a glance

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

Density modification of cryo-EM maps

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

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

Evidence of functional protein dynamics from X-ray crystallographic ensembles

FEM: feature-enhanced map.

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

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

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

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

Graphical tools for macromolecular crystallography in PHENIX

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

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

Improved crystallographic structures using extensive combinatorial refinement

Improvement of cryo-EM maps by density modification

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

Interactive comparison and remediation of collections of macromolecular structures.

Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models

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

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

Joint X-ray and neutron refinement with phenix.refine

Learning About Biomolecular Solvation from Water in Protein Crystals

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

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

Metrics for comparison of crystallographic maps

Model morphing and sequence assignment after molecular replacement

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 ⬇️

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

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

On macromolecular refinement at subatomic resolution with interatomic scatterers

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

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

On the use of logarithmic scales for analysis of diffraction data

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

Polder maps: improving OMIT maps by excluding bulk solvent.

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

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

Programming new geometry restraints: parallelity of atomic groups

Protein structures by spallation neutron crystallography.

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

Q|R: quantum-based refinement

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

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

Recent developments in phasing and structure refinement for macromolecular crystallography

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

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

Structure and membrane remodeling activity of ESCRT-III helical polymers

Structure of photosystem II and substrate binding at room temperature.

TLS from fundamentals to practice

The Phenix software for automated determination of macromolecular structures

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

The solvent component of macromolecular crystals.

Towards automated crystallographic structure refinement with phenix.refine

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

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

Visualizing chaperone-assisted protein folding.

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

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

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