User profiles for Paul Adams

Paul D. Adams

Lawrence Berkeley Laboratory & University of California Berkeley
Verified email at lbl.gov
Cited by 121670

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

PD Adams, PV Afonine, G Bunkóczi… - … Section D: Biological …, 2010 - scripts.iucr.org
Macromolecular X-ray crystallography is routinely applied to understand biological processes
at a molecular level. However, significant time and effort are still required to solve and …

Crystallography & NMR system: A new software suite for macromolecular structure determination

AT Brünger, PD Adams, GM Clore… - … Section D: Biological …, 1998 - scripts.iucr.org
A new software suite, called Crystallography & NMR System (CNS), has been developed for
macromolecular structure determination by X-ray crystallography or solution nuclear …

[HTML][HTML] PHENIX: building new software for automated crystallographic structure determination

PD Adams, RW Grosse-Kunstleve, LW Hung… - … Section D: Biological …, 2002 - iucr.org
Structural genomics seeks to expand rapidly the number of protein structures in order to
extract the maximum amount of information from genomic sequence databases. The advent of …

Improvement of cryo-EM maps by density modification

TC Terwilliger, SJ Ludtke, RJ Read, PD Adams… - Nature …, 2020 - nature.com
A density-modification procedure for improving maps from single-particle electron cryogenic
microscopy (cryo-EM) is presented. The theoretical basis of the method is identical to that of …

Accurate prediction of protein structures and interactions using a three-track neural network

…, LN Kinch, RD Schaeffer, C Millán, H Park, C Adams… - Science, 2021 - science.org
DeepMind presented notably accurate predictions at the recent 14th Critical Assessment of
Structure Prediction (CASP14) conference. We explored network architectures that …

[HTML][HTML] Phaser crystallographic software

AJ McCoy, RW Grosse-Kunstleve, PD Adams… - Journal of applied …, 2007 - iucr.org
Phaser is a program for phasing macromolecular crystal structures by both molecular
replacement and experimental phasing methods. The novel phasing algorithms implemented in …

[HTML][HTML] Towards automated crystallographic structure refinement with phenix. refine

…, A Urzhumtsev, PH Zwart, PD Adams - … Section D: Biological …, 2012 - scripts.iucr.org
phenix.refine is a program within the PHENIX package that supports crystallographic structure
refinement against experimental data with a wide range of upper resolution limits using a …

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

…, LL Videau, CJ Williams, PD Adams - … Section D: Structural …, 2019 - scripts.iucr.org
Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful
methods to determine three-dimensional macromolecular structures, which are required to …

MolProbity: More and better reference data for improved all‐atom structure validation

…, WB Arendall III, J Snoeyink, PD Adams… - Protein …, 2018 - Wiley Online Library
This paper describes the current update on macromolecular model validation services that
are provided at the MolProbity website, emphasizing changes and additions since the …

[HTML][HTML] Real-space refinement in PHENIX for cryo-EM and crystallography

…, TC Terwilliger, A Urzhumtsev, PD Adams - … Section D: Structural …, 2018 - scripts.iucr.org
This article describes the implementation of real-space refinement in the phenix.real_space_refine
program from the PHENIX suite. The use of a simplified refinement target function …