Paul D. Adams

发表

Protein crystallography automation software at the Advanced Light Source

John R. Taylor, Nicholas K. Sauter, Carl W. Cork, 2003 .

An Application of Cartesian-Grid and Volume-of-Fluid Methods to Numerical Ship Hydrodynamics

Paul D. Adams, Mark Sussman, Thomas T. O'Shea, 2007 .

The PSI SGKB Technology Portal - An Online Database of Structural Genomics Technologies

Helen M. Berman, Paul D. Adams, Lester G. Carter, 2010 .

REFINAMIENTO DE ESTRUCTURAS MACROMOLECULARES CRISTALOGRÁFICAS MACROMOLECULAR CRYSTALLOGRAPHIC STRUCTURE REFINEMENT

Paul D. Adams, Pavel V. Afonine, Alexandre Urzhumtsev, 2015 .

Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns

Nicholas K. Sauter, Paul D. Adams, Nathaniel Echols, 2015, Acta crystallographica. Section D, Biological crystallography.

Graphical tools for macromolecular crystallography in PHENIX

Randy J. Read, Airlie J. McCoy, Paul D. Adams, 2012, Journal of applied crystallography.

A rapid methods development workflow for high-throughput quantitative proteomic applications

Paul D. Adams, Jay D. Keasling, Yan Chen, 2019, PloS one.

The Structural Biology Knowledgebase – structures, functions, methods and more

John D. Westbrook, Helen M. Berman, Paul D. Adams, 2011 .

LABELIT: Robust Indexing for Automatic Data Collection

Nicholas K. Sauter, Paul D. Adams, Ralf W. Grosse-Kunstleve, 2004 .

cctbx news: Phil and friends

Nicholas K. Sauter, Paul D. Adams, Ralf W. Grosse-Kunstleve, 2005 .

Standard Flow Liquid Chromatography for Shotgun Proteomics in Bioenergy Research

Paul D. Adams, Joshua L. Heazlewood, Leanne Jade G. Chan, 2015, Front. Bioeng. Biotechnol..

Quantitative Proteomics for Metabolically Engineered Biofuel Pathway Optimization

Paul D. Adams, Jay D. Keasling, Aindrila Mukhopadhyay, 2009 .

High Throughput Technologies to Break the Biological Barriers to Cellulosic Fuels

Paul D. Adams, Huu Tran, Masood Z. Hadi, 2009 .

State of the Toolbox: An overview of the Computational Crystallography Toolbox (CCTBX)

Paul D. Adams, Ralf W. Grosse-Kunstleve, 2003 .

Microfluidic assays for biofuels research

Paul D. Adams, Blake A. Simmons, Aarthi Chandrasekaran, 2011 .

A Peptide-Based Method for 13C Metabolic Flux Analysis in Microbial Communities

Paul D. Adams, Amit Ghosh, Daniel Weaver, 2014, PLoS Comput. Biol..

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

Paul D. Adams, Nathaniel Echols, Ralf W. Grosse-Kunstleve, 2012, Acta crystallographica. Section D, Biological crystallography.

Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution

Genki Terashi, Daisuke Kihara, Grigore D. Pintilie, 2020, bioRxiv.

L3 Interactive Data Language

Paul D. Adams, Michael Hohn, 2006 .

Programs and program systems in wide use

Randy J. Read, Paul D. Adams, Anastassis Perrakis, 2006 .

Electronic Reprint Applied Crystallography Automatic Multiple-zone Rigid-body Refinement with a Large Convergence Radius Pavel v. Afonine Et Al. · Automatic Multiple-zone Rigid-body Refinement Applied Crystallography Automatic Multiple-zone Rigid-body Refinement with a Large Convergence Radius

Paul D. Adams, Ralf W. Grosse-Kunstleve, Pavel V. Afonine, 2008 .

The protein structure initiative structural genomics knowledgebase

John D. Westbrook, Helen M. Berman, Paul D. Adams, 2008, Nucleic Acids Res..

Enhanced macromolecular refinement by simulated annealing

Paul D. Adams, Luke M. Rice, Axel T. Brunger, 2006 .

Evidence of Functional Protein Dynamics from X-Ray Crystallographic Ensembles

Paul D. Adams, Pavel V. Afonine, Teresa Head-Gordon, 2010, PLoS Comput. Biol..

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

Paul D. Adams, Pavel V. Afonine, Thomas C. Terwilliger, 2018, bioRxiv.

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

Paul D. Adams, Pavel V. Afonine, Alexandre Urzhumtsev, 2016, Acta Crystallographica. Section D, Structural Biology.

Characterization of X-ray data sets

Paul D. Adams, Peter H. Zwart, Ralf W. Grosse-Kunsteleve, 2005 .

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

Randy J. Read, Paul D. Adams, Pavel V. Afonine, 2018 .

Towards an Automated Data Collection Pipeline

Nicholas K. Sauter, Carl W. Cork, Earl W. Cornell, 2002 .

The Computational Crystallography Toolbox: crystallographic algorithms in a reusable software framework

Nicholas K. Sauter, Paul D. Adams, Ralf W. Grosse-Kunstleve, 2002 .

Microfluidic Technology for Biofuels Applications

Paul D. Adams, Anup K. Singh, Aarthi Chandrasekaran, 2009 .

An editor for the generation and customization of geometry restraints

Paul D. Adams, Nigel W. Moriarty, Eli J. Draizen, 2017, Acta crystallographica. Section D, Structural biology.

Acta Crystallographica Section D Biological

Randy J. Read, Airlie J. McCoy, Paul D. Adams, 2003 .

cctbx news: Fast triplet generator for direct methods, gallery of direct-space asymmetric units, et. al.

Paul D. Adams, Ralf W. Grosse-Kunstleve, Buddy Wong, 2003 .

Phenix - a comprehensive python-based system for macromolecular structure solution

Randy J. Read, Airlie J. McCoy, Paul D. Adams, 2012 .

Crystallographic Structure Refinement in a Nutshell

Paul D. Adams, Pavel V. Afonine, P. Adams, 2013 .

A New Generation of Crystallographic Validation Tools for the Protein Data Bank

Randy J. Read, Paul D. Adams, Gerard J. Kleywegt, 2011, Structure.

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

Randy J. Read, Paul D. Adams, Michael Levitt, 2012, Acta crystallographica. Section D, Biological crystallography.

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

Randy J. Read, Paul D. Adams, Ralf W. Grosse-Kunstleve, 2007 .

Combining Crystallographic and Structure-Modeling Approaches in Macromolecular Crystallography

Randy J. Read, Paul D. Adams, David Baker, 2014 .

Personal Computer, VDT Use Increases in Journalism Classes

Paul D. Adams, 1987 .

Improved ligand geometries in crystallographic refinement using AFITT in PHENIX

Paul D. Adams, David A. Case, Darrin M. York, 2016, Acta crystallographica. Section D, Structural biology.

Automated map sharpening by maximization of detail and connectivity

Paul D. Adams, Pavel V. Afonine, Thomas C. Terwilliger, 2018 .

Robust Indexing and Automatic Data Collection at the Advanced Light Source

John R. Taylor, Nicholas K. Sauter, Carl W. Cork, 2004 .

The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource

Helen M. Berman, Paul D. Adams, Lester G. Carter, 2012, Journal of Structural and Functional Genomics.

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

Randy J. Read, Paul D. Adams, Nathaniel Echols, 2012, Journal of Structural and Functional Genomics.

Technologies for Characterizing Molecular and Cellular Systems Relevant to Bioenergy and Environment. Workshop report, September 21–23, 2016

Paul D. Adams, Todd Anderson, Elizabeth R. Wright, 2017 .

Hybrid programming in crystallography: phenix.refine and phenix.hyss

Paul D. Adams, Ralf W. Grosse-Kunstleve, Pavel V. Afonine, 2005 .

iotbx.cif: a comprehensive CIF toolbox

Paul D. Adams, Ralf W. Grosse-Kunstleve, Richard J. Gildea, 2011, Journal of applied crystallography.

A Microscale Platform for Integrated Cell-Free Expression and Screening of Cellulase Activity

Paul D. Adams, Anup K. Singh, Aarthi Chandrasekaran, 2009 .

Advances, Interactions, and Future Developments in the CNS, Phenix, and Rosetta Structural Biology Software Systems Annual Review of Biophysics

Randy J. Read, Paul D. Adams, David Baker, 2012 .

The PHENIX graphical user interface

Nicholas K. Sauter, Paul D. Adams, Ralf W. Grosse-Kunstleve, 2002 .

Automated structure determination with phenix

Randy J. Read, Airlie J. McCoy, Laurent C. Storoni, 2006 .

Science-Driven Network Requirements for ESnet

Dean N. Williams, Paul D. Adams, Michael F. Wehner, 2006 .

Automatic Fortran to C++ conversion with FABLE

Nicholas K. Sauter, Paul D. Adams, Ralf W. Grosse-Kunstleve, 2012, Source Code for Biology and Medicine.

Phaser crystallographic software

Randy J. Read, Airlie J. McCoy, Laurent C. Storoni, 2007, Journal of applied crystallography.

A More Automated Approach to Data Collection for Macromolecular Crystallography

Nicholas K. Sauter, Paul D. Adams, Peter H. Zwart, 2008 .

CHAPTER 3:Overcoming Data Processing Challenges for Breakthrough Crystallography

Nicholas K. Sauter, Paul D. Adams, 2017 .

PSI SBKB Technology Portal: A Structural Biology Web Resource

Helen M. Berman, Paul D. Adams, Margaret Gabanyi, 2015 .

Structural Genomics of Minimal Organisms and Protein Fold Space

Paul D. Adams, Steven E. Brenner, Stephen R. Holbrook, 2005, Journal of Structural and Functional Genomics.

Ensemble refinement of protein crystal structures inPHENIX

Paul D. Adams, Pavel V. Afonine, Piet Gros, 2011 .

Programming new geometry restraints: parallelity of atomic groups

Paul D. Adams, Pavel V. Afonine, Alexandre Urzhumtsev, 2015, Journal of applied crystallography.

Exploring Metric Symmetry

Paul D. Adams, Ralf W. Grosse-Kunstleve, Petrus H. Zwart, 2006 .

Robust indexing for automatic data collection

Nicholas K. Sauter, Paul D. Adams, Ralf W. Grosse-Kunstleve, 2004, Journal of applied crystallography.

Electronic Reprint Biological Crystallography Decision-making in Structure Solution Using Bayesian Estimates of Map Quality: the Phenix Autosol Wizard Biological Crystallography Decision-making in Structure Solution Using Bayesian Estimates of Map Quality: the Phenix Autosol Wizard

Randy J. Read, Airlie J. McCoy, Paul D. Adams, 2022 .

Biochemical and Structural Studies of NADH-Dependent FabG Used To Increase the Bacterial Production of Fatty Acids under Anaerobic Conditions

Paul D. Adams, Jay D. Keasling, Ee-Been Goh, 2013, Applied and Environmental Microbiology.

Structures of the intermediates of Kok’s photosynthetic water oxidation clock

Nicholas K. Sauter, Paul D. Adams, Sébastien Boutet, 2018, Nature.

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

Randy J. Read, Paul D. Adams, Ralf W. Grosse-Kunstleve, 2008, Acta crystallographica. Section D, Biological crystallography.

Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models

Randy J. Read, Paul D. Adams, Ralf W. Grosse-Kunstleve, 2007, Acta crystallographica. Section D, Biological crystallography.

Automated flow-based/digital microfluidic platform integrated with onsite electroporation process for multiplex genetic engineering applications

Paul D. Adams, David Ando, Hector Garcia Martin, 2018, 2018 IEEE Micro Electro Mechanical Systems (MEMS).

FEM: feature-enhanced map

Paul D. Adams, Pavel V. Afonine, Alexandre Urzhumtsev, 2014, Acta crystallographica. Section D, Biological crystallography.

Ligand identification using electron-density map correlations

Judith D. Cohn, Paul D. Adams, Nigel W. Moriarty, 2006, Acta crystallographica. Section D, Biological crystallography.

Molecular Dynamics Applied to X‐Ray Structure Refinement

Paul D. Adams, Axel T. Brunger, 2002 .

On macromolecular refinement at subatomic resolution with interatomic scatterers

Paul D. Adams, Ralf W. Grosse-Kunstleve, Pavel V. Afonine, 2007, Acta Crystallographica Section D: Biological Crystallography.

Development of a Native Escherichia coli Induction System for Ionic Liquid Tolerance

Paul D. Adams, Blake A. Simmons, Jay D. Keasling, 2014, PloS one.

Coupling of Receptor Conformation and Ligand Orientation Determine Graded Activity

Min Zhao, Paul D. Adams, Pavel V. Afonine, 2010, Nature chemical biology.

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

Paul D. Adams, Wen Jiang, Wah Chiu, 2017, Proceedings of the National Academy of Sciences.

Metrics for comparison of crystallographic maps

Paul D. Adams, Pavel V. Afonine, Alexandre Urzhumtsev, 2014, Acta crystallographica. Section D, Biological crystallography.

Structure of photosystem II and substrate binding at room temperature

Marcin Sikorski, Nicholas K. Sauter, Paul D. Adams, 2016, Nature.

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

Randy J. Read, Paul D. Adams, Ralf W. Grosse-Kunstleve, 2012, Acta crystallographica. Section D, Biological crystallography.

short communications Acta Crystallographica Section D Biological

Paul D. Adams, Pavel V. Afonine, Alexandre Urzhumtsev, 1998 .

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

Paul D. Adams, Pavel V. Afonine, Alexandre Urzhumtsev, 2018, bioRxiv.

Taking Snapshots of Photosynthetic Water Oxidation Using Femtosecond X-ray Diffraction and Spectroscopy

Nicholas K. Sauter, Paul D. Adams, Sébastien Boutet, 2014, Nature Communications.

CryoEM Models and Associated Data Submitted to the 2015/2016 EMDataBank Model Challenge

Takeshi Kawabata, Haruki Nakamura, Genki Terashi, 2018 .

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

Paul D. Adams, Nathaniel Echols, Nigel W. Moriarty, 2013, Acta crystallographica. Section D, Biological crystallography.

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

Paul D. Adams, Pavel V. Afonine, Thomas C. Terwilliger, 2018, bioRxiv.

A robust bulk-solvent correction and anisotropic scaling procedure

Paul D. Adams, Ralf W. Grosse-Kunstleve, Pavel V. Afonine, 2005, Acta crystallographica. Section D, Biological crystallography.

Crystal Structures of a Group II Chaperonin Reveal the Open and Closed States Associated with the Protein Folding Cycle*♦

Paul D. Adams, Corie Y. Ralston, J. H. Pereira, 2010, The Journal of Biological Chemistry.

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

Judith D. Cohn, Paul D. Adams, Nigel W. Moriarty, 2006, Acta crystallographica. Section D, Biological crystallography.

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

Paul D. Adams, Nathaniel Echols, Pavel V. Afonine, 2014, Acta crystallographica. Section D, Biological crystallography.

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

Matthew L. Baker, Paul D. Adams, Dong-Hua Chen, 2014, Nature Communications.

Polder maps: improving OMIT maps by excluding bulk solvent

Paul D. Adams, Pavel V. Afonine, Nigel W. Moriarty, 2017, Acta crystallographica. Section D, Structural biology.

Model morphing and sequence assignment after molecular replacement

Randy J. Read, Paul D. Adams, Pavel V. Afonine, 2013, Acta crystallographica. Section D, Biological crystallography.

Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules

Paul D. Adams, Pavel V. Afonine, Paul Langan, 2009, Acta crystallographica. Section D, Biological crystallography.

Experience converting a large Fortran-77 program to C + +

Paul D. Adams, Ralf W. Grosse-Kunstleve, Thomas C. Terwilliger, 2009 .

Improved statistics for determining the Patterson symmetry from unmerged diffraction intensities

Nicholas K. Sauter, Paul D. Adams, Ralf W. Grosse-Kunstleve, 2006 .

On the handling of atomic anisotropic displacement parameters

Paul D. Adams, Ralf W. Grosse-Kunstleve, P. Adams, 2002 .

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

Paul D. Adams, Thomas C. Terwilliger, Peter H. Zwart, 2016, Acta crystallographica. Section D, Structural biology.

Macromolecular refinement of X-ray and cryo-electron microscopy structures with Phenix / OPLS3e for improved structure and ligand quality

Paul D. Adams, Nigel W. Moriarty, Oleg V. Sobolev, 2020, bioRxiv.

Averaged kick maps: less noise, more signal…and probably less bias

Paul D. Adams, Pavel V. Afonine, Jure Pražnikar, 2009, Acta crystallographica. Section D, Biological crystallography.

New Science Opportunities Enabled by LCLS-II X-ray Lasers

Anton Barty, Sebastian Doniach, Paul D. Adams, 2015 .

Predicting X-ray Diffuse Scattering from Translation Libration Screw Structural Ensembles

Michael E. Wall, Nicholas K. Sauter, Paul D. Adams, 2015 .

Computational searching and mutagenesis suggest a structure for the pentameric transmembrane domain of phospholamban

Paul D. Adams, Isaiah T. Arkin, Axel T. Brünger, 1995, Nature Structural Biology.

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

Paul D. Adams, Ralf W. Grosse-Kunstleve, Pavel V. Afonine, 2010, Journal of applied crystallography.

Phaser.MRage: automated molecular replacement

Randy J. Read, Airlie J. McCoy, Paul D. Adams, 2013, Acta crystallographica. Section D, Biological crystallography.

The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods

John D. Westbrook, Helen M. Berman, Paul D. Adams, 2011, Journal of Structural and Functional Genomics.

Automated identification of elemental ions in macromolecular crystal structures

Randy J. Read, Airlie J. McCoy, Paul D. Adams, 2014, Acta crystallographica. Section D, Biological crystallography.