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List of works by Paul D. Adams

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Phasercrystallographic software

scientific article (publication date: August 2007)
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)
Towards automated crystallographic structure refinement with phenix.refine

scientific article (publication date: April 2012)
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard

scientific article (publication date: 2008)
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard

scientific article (publication date: June 2009)
The Phenix software for automated determination of macromolecular structures

scientific article (publication date: September 2011)
Structural basis for double-stranded RNA processing by Dicer

scientific article
SPARX, a new environment for Cryo-EM image processing

scientific article published on 16 July 2006
EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy.

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

scientific article published on 30 May 2018
A new generation of crystallographic validation tools for the protein data bank

scientific article
MolProbity: More and better reference data for improved all-atom structure validation

scientific article published on 25 October 2017
A dimerization motif for transmembrane α–helices

scientific article published on 01 March 1994
Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature

scientific article
Engineering dynamic pathway regulation using stress-response promoters.

scientific article
Substructure search procedures for macromolecular structures

scientific article (publication date: November 2003)
Joint X-ray and neutron refinement with phenix.refine

scientific article
Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production

scientific article published on 29 May 2013
Computational searching and mutagenesis suggest a structure for the pentameric transmembrane domain of phospholamban

scientific article published on 01 February 1995
Polder maps: improving OMIT maps by excluding bulk solvent.

scientific article published on February 2017
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

scientific article published on 02 October 2019
Crystal structure of a bacterial ribonuclease P RNA.

scientific article
Modelling dynamics in protein crystal structures by ensemble refinement

scientific article
Nanoflow electrospinning serial femtosecond crystallography

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

scientific article published on 16 March 2012
Robust indexing for automatic data collection

scientific article
New applications of simulated annealing in X-ray crystallography and solution NMR.

scientific article published on March 1997
Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules

scientific article published on 15 May 2009
New tools for the analysis and validation of cryo-EM maps and atomic models

scientific article published on 03 September 2018
Room temperature femtosecond X-ray diffraction of photosystem II microcrystals

scientific article
Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers

scientific article
Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy.

scientific article
Improved low-resolution crystallographic refinement with Phenix and Rosetta

scientific article
Enhancing fatty acid production by the expression of the regulatory transcription factor FadR.

scientific article published on 28 September 2012
Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias

scientific article published on 19 April 2008
Experimentally based orientational refinement of membrane protein models: A structure for the Influenza A M2 H+ channel

scientific article
Structure of photosystem II and substrate binding at room temperature

scientific article
Targeted proteomics for metabolic pathway optimization: application to terpene production

scientific article published on 5 January 2011
FEM: feature-enhanced map.

scientific article
Phaser.MRage: automated molecular replacement

scientific article (publication date: November 2013)
Graphical tools for macromolecular crystallography in PHENIX

scientific article
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

scientific article published on 18 June 2015
An atomic model of brome mosaic virus using direct electron detection and real-space optimization

scientific article
Crystallographic model quality at a glance

scientific article published on 20 February 2009
Error Rate Comparison during Polymerase Chain Reaction by DNA Polymerase

scientific article
The protein structure initiative structural genomics knowledgebase

scientific article
Use of a new label, (13)==(18)O, in the determination of a structural model of phospholamban in a lipid bilayer. Spatial restraints resolve the ambiguity arising from interpretations of mutagenesis data.

scientific article published in July 2000
Role of the -phosphate of ATP in triggering protein folding by GroEL-GroES: function, structure and energetics

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

scientific article published on 28 February 2013

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