List of works - Thomas C. Terwilliger

1.55 Å resolution X-ray crystal structure of Rv3902c fromMycobacterium tuberculosis

scientific article

A Suite of Engineered GFP Molecules for Oligomeric Scaffolding

scientific article

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

scientific article published on 30 October 2018

A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis.

scientific article

A high-throughput immobilized bead screen for stable proteins and multi-protein complexes

scientific article

A monomeric mycobacteriophage immunity repressor utilizes two domains to recognize an asymmetric DNA sequence

scientific article published in 2022

A new protein-protein interaction sensor based on tripartite split-GFP association

scientific article

Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems

scientific article published on 28 February 2013

An automated high-throughput screening method for the identification of high-yield, soluble protein variants using cell-free expression and systematic truncation

scientific article published in December 2006

Analysis of nucleoside-binding proteins by ligand-specific elution from dye resin: application to Mycobacterium tuberculosis aldehyde dehydrogenases

scientific article

Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum

scientific article

Archiving raw crystallographic data

scientific article

Automated identification of elemental ions in macromolecular crystal structures

scientific article published on 20 March 2014

Automated ligand fitting by core-fragment fitting and extension into density

scientific article published on 18 July 2006

Automated structure determination with phenix

Automated, high-throughput platform for protein solubility screening using a split-GFP system

scientific article

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

scientific article published on 25 December 2013

Bottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieu

scientific article published on 25 November 2019

Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing.

scientific article published on March 2016

Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal.

scientific article

Chemical shift assignments for Rv0577, a putative glyoxylase associated with virulence from Mycobacterium tuberculosis

scientific article

Combining Crystallographic and Structure-Modeling Approaches in Macromolecular Crystallography

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

Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering

scientific article

Context dependence of mutational effects in a protein: the crystal structures of the V35I, I47V and V35I/I47V gene V protein core mutants

scientific article

Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data

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

Crystal structure of AcrB complexed with linezolid at 3.5 Å resolution

scientific article

Crystal structure of Bacillus subtilis GabR, an autorepressor and transcriptional activator of gabT

scientific article

Crystal structure of a putative pyridoxine 5'-phosphate oxidase (Rv2607) from Mycobacterium tuberculosis

scientific article published in March 2006

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

Domain Orientation in the Inactive Response Regulator Mycobacterium tuberculosis MtrA Provides a Barrier to Activation † , ‡

scientific article

Efficient merging of data from multiple samples for determination of anomalous substructure

scientific article

Engineering and characterization of a superfolder green fluorescent protein

scientific article

Enhancement of crystallization with nucleotide ligands identified by dye-ligand affinity chromatography

scientific article

Experimental mapping of soluble protein domains using a hierarchical approach

scientific article

FEM: feature-enhanced map.

scientific article

Finding non-crystallographic symmetry in density maps of macromolecular structures ⬇️

scientific article published on July 24, 2013

Functional and structural characterization of a thiol peroxidase from Mycobacterium tuberculosis

scientific journal article

Functional linkages can reveal protein complexes for structure determination

scientific article published on September 2007

Graphical tools for macromolecular crystallography in PHENIX

scientific article

Improved AlphaFold modeling with implicit experimental information

scientific article published in 2022

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

Improved low-resolution crystallographic refinement with Phenix and Rosetta

scientific article

Improved molecular replacement by density- and energy-guided protein structure optimization

scientific article (publication date: 26 May 2011)

Improvement of cryo-EM maps by density modification

scientific article published on 17 August 2020

Improving experimental phases for strong reflections prior to density modification

scientific article published on 20 September 2013

Inaugural structure from the DUF3349 superfamily of proteins, Mycobacterium tuberculosis Rv0543c ⬇️

scientific article published on December 6, 2010

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

Lessons from structural genomics

scientific article (publication date: 2009)

Ligand identification using electron-density map correlations

scientific article published on 13 December 2006

Ligand placement based on prior structures: the guided ligand-replacement method

scientific article published on 25 December 2013

MAD phasing: Bayesian estimates of F(A).

scientific article published in January 1994

Macromolecular X-ray structure determination using weak, single-wavelength anomalous data

scientific article

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

scientific article published on 02 October 2019

Metrics for comparison of crystallographic maps

scientific article

Model morphing and sequence assignment after molecular replacement

scientific article published on 18 October 2013

New molecular reporters for rapid protein folding assays

scientific article

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

scientific article published on 03 September 2018

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop

scientific article

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

scientific article

PHENIX: building new software for automated crystallographic structure determination

scientific article (publication date: November 2002)

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

scientific article

Protein Crystallography from the Perspective of Technology Developments

scientific article

Protein production and purification

scientific article

Publisher Correction: A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis

scientific article published on 19 November 2020

RIKEN aids international structural genomics efforts

scientific article published in January 2007

RNA Structure Refinement Using the ERRASER-Phenix Pipeline

scientific article published on January 2016

Rapid chain tracing of polypeptide backbones in electron-density maps

scientific article

Rapid model building of alpha-helices in electron-density maps

scientific article

Rapid model building of beta-sheets in electron-density maps

scientific article

Raw diffraction data preservation and reuse: overview, update on practicalities and metadata requirements.

scientific article

Recent developments in phasing and structure refinement for macromolecular crystallography

scientific article published on 21 August 2009

Relationship between in vivo activity and in vitro measures of function and stability of a protein

scientific article

Solution structure of Rv2377c-founding member of the MbtH-like protein family

scientific article

Solution structure of the conserved hypothetical protein Rv2302 from Mycobacterium tuberculosis.

scientific article

Split green fluorescent protein as a modular binding partner for protein crystallization

scientific article

Structural biology. Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli

scientific article

Structure of Mycobacterium tuberculosis RuvA, a protein involved in recombination

scientific article

Structure of Rv1848 (UreA), the Mycobacterium tuberculosis urease gamma subunit

scientific article

Structure of translation initiation factor 5A from Pyrobaculum aerophilum at 1.75 A resolution

scientific article

Subfamily-specific adaptations in the structures of two penicillin-binding proteins from Mycobacterium tuberculosis

scientific article

The Phenix software for automated determination of macromolecular structures

scientific article (publication date: September 2011)

The TB Structural Genomics Consortium: a decade of progress

scientific article published on 17 January 2011

The optimization of in vitro high-throughput chemical lysis of Escherichia coli. Application to ACP domain of the polyketide synthase ppsC from Mycobacterium tuberculosis

scientific article

The success of structural genomics ⬇️

scientific article published on June 17, 2011

Towards automated crystallographic structure refinement with phenix.refine

scientific article (publication date: April 2012)

X-ray structure determination using low-resolution electron microscopy maps for molecular replacement

scientific article

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

scientific article

List of works by Thomas C. Terwilliger

1.55 Å resolution X-ray crystal structure of Rv3902c fromMycobacterium tuberculosis

A Suite of Engineered GFP Molecules for Oligomeric Scaffolding

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

A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis.

A high-throughput immobilized bead screen for stable proteins and multi-protein complexes

A monomeric mycobacteriophage immunity repressor utilizes two domains to recognize an asymmetric DNA sequence

A new protein-protein interaction sensor based on tripartite split-GFP association

Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems

An automated high-throughput screening method for the identification of high-yield, soluble protein variants using cell-free expression and systematic truncation

Analysis of nucleoside-binding proteins by ligand-specific elution from dye resin: application to Mycobacterium tuberculosis aldehyde dehydrogenases

Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum

Archiving raw crystallographic data

Automated identification of elemental ions in macromolecular crystal structures

Automated ligand fitting by core-fragment fitting and extension into density

Automated structure determination with phenix

Automated, high-throughput platform for protein solubility screening using a split-GFP system

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

Bottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieu

Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing.

Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal.

Chemical shift assignments for Rv0577, a putative glyoxylase associated with virulence from Mycobacterium tuberculosis

Combining Crystallographic and Structure-Modeling Approaches in Macromolecular Crystallography

Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering

Context dependence of mutational effects in a protein: the crystal structures of the V35I, I47V and V35I/I47V gene V protein core mutants

Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data

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

Crystal structure of AcrB complexed with linezolid at 3.5 Å resolution

Crystal structure of Bacillus subtilis GabR, an autorepressor and transcriptional activator of gabT

Crystal structure of a putative pyridoxine 5'-phosphate oxidase (Rv2607) from Mycobacterium tuberculosis

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

Density modification of cryo-EM maps

Domain Orientation in the Inactive Response Regulator Mycobacterium tuberculosis MtrA Provides a Barrier to Activation † , ‡

Efficient merging of data from multiple samples for determination of anomalous substructure

Engineering and characterization of a superfolder green fluorescent protein

Enhancement of crystallization with nucleotide ligands identified by dye-ligand affinity chromatography

Experimental mapping of soluble protein domains using a hierarchical approach

FEM: feature-enhanced map.

Finding non-crystallographic symmetry in density maps of macromolecular structures ⬇️

Functional and structural characterization of a thiol peroxidase from Mycobacterium tuberculosis

Functional linkages can reveal protein complexes for structure determination

Graphical tools for macromolecular crystallography in PHENIX

Improved AlphaFold modeling with implicit experimental information

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

Improved crystallographic structures using extensive combinatorial refinement

Improved low-resolution crystallographic refinement with Phenix and Rosetta

Improved molecular replacement by density- and energy-guided protein structure optimization

Improvement of cryo-EM maps by density modification

Improving experimental phases for strong reflections prior to density modification

Inaugural structure from the DUF3349 superfamily of proteins, Mycobacterium tuberculosis Rv0543c ⬇️

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

Lessons from structural genomics

Ligand identification using electron-density map correlations

Ligand placement based on prior structures: the guided ligand-replacement method

MAD phasing: Bayesian estimates of F(A).

Macromolecular X-ray structure determination using weak, single-wavelength anomalous data

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

Metrics for comparison of crystallographic maps

Model morphing and sequence assignment after molecular replacement

New molecular reporters for rapid protein folding assays

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

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop

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

PHENIX: building new software for automated crystallographic structure determination

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

Protein Crystallography from the Perspective of Technology Developments

Protein production and purification

Publisher Correction: A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis

RIKEN aids international structural genomics efforts

RNA Structure Refinement Using the ERRASER-Phenix Pipeline

Rapid chain tracing of polypeptide backbones in electron-density maps

Rapid model building of alpha-helices in electron-density maps

Rapid model building of beta-sheets in electron-density maps

Raw diffraction data preservation and reuse: overview, update on practicalities and metadata requirements.

Recent developments in phasing and structure refinement for macromolecular crystallography

Relationship between in vivo activity and in vitro measures of function and stability of a protein

Solution structure of Rv2377c-founding member of the MbtH-like protein family