Paul D. Adams

Physical Biosciences Division, Lawrence Berkeley National Laboratory

Affiliated withLawrence Berkeley National Laboratory

Research Area

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 4	2010

Other Publications

Article	Year
Molecular dynamics applied to X-ray structure refinement. Accounts of chemical research\| PubMed ID: 12069625	2002
Alpha(IIb)beta(3) 整合素的跨膜信号转导。 Protein science : a publication of the Protein Society\| PubMed ID: 12070332	2002
Intramolecular quenching of tryptophan fluorescence by the peptide bond in cyclic hexapeptides. Journal of the American Chemical Society\| PubMed ID: 12149035	2002
PHENIX: building new software for automated crystallographic structure determination. Acta crystallographica. Section D, Biological crystallography\| PubMed ID: 12393927	2002
Fluorescence of cis-1-amino-2-(3-indolyl)cyclohexane-1-carboxylic acid: a single tryptophan chi(1) rotamer model. Journal of the American Chemical Society\| PubMed ID: 12405862	2002
Computational aspects of high-throughput crystallographic macromolecular structure determination. Methods of biochemical analysis\| PubMed ID: 12647382	2003
High-resolution structure of RNase P protein from Thermotoga maritima. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 12799461	2003
X-ray crystallographic and kinetic studies of human sorbitol dehydrogenase. Structure (London, England : 1993)\| PubMed ID: 12962626	2003
Role of the gamma-phosphate of ATP in triggering protein folding by GroEL-GroES: function, structure and energetics. The EMBO journal\| PubMed ID: 14517228	2003
Recent developments in the PHENIX software for automated crystallographic structure determination. Journal of synchrotron radiation\| PubMed ID: 14646133	2004
Crystal structures of the Rhodococcus proteasome with and without its pro-peptides: implications for the role of the pro-peptide in proteasome assembly. Journal of molecular biology\| PubMed ID: 14659753	2004
Automatic solution of heavy-atom substructures. Methods in enzymology\| PubMed ID: 14696368	2003
Backbone dynamics of an oncogenic mutant of Cdc42Hs shows increased flexibility at the nucleotide-binding site. Biochemistry\| PubMed ID: 15287724	2004
Exploring the structural dynamics of the E.coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states. Journal of molecular biology\| PubMed ID: 15313620	2004
Crystal structure of a PhoU protein homologue: a new class of metalloprotein containing multinuclear iron clusters. The Journal of biological chemistry\| PubMed ID: 15716271	2005
Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 15728358	2005
Crystal structure of the "PhoU-like" phosphate uptake regulator from Aquifex aeolicus. Journal of bacteriology\| PubMed ID: 15937186	2005
Crystal structure of a heat-inducible transcriptional repressor HrcA from Thermotoga maritima: structural insight into DNA binding and dimerization. Journal of molecular biology\| PubMed ID: 15979091	2005
A robust bulk-solvent correction and anisotropic scaling procedure. Acta crystallographica. Section D, Biological crystallography\| PubMed ID: 15983406	2005
Crystal structure of a bacterial ribonuclease P RNA. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 16157868	2005
Automated crystallographic ligand building using the medial axis transform of an electron-density isosurface. Acta crystallographica. Section D, Biological crystallography\| PubMed ID: 16204887	2005
Structural genomics of minimal organisms and protein fold space. Journal of structural and functional genomics\| PubMed ID: 16211501	2005
Crystal structures of an NAD kinase from Archaeoglobus fulgidus in complex with ATP, NAD, or NADP. Journal of molecular biology\| PubMed ID: 16242716	2005
Structural basis for double-stranded RNA processing by Dicer. Science (New York, N.Y.)\| PubMed ID: 16410517	2006
Solution structure of an oncogenic mutant of Cdc42Hs. Biochemistry\| PubMed ID: 16489751	2006
Automated ligand fitting by core-fragment fitting and extension into density. Acta crystallographica. Section D, Biological crystallography\| PubMed ID: 16855309	2006
SPARX, a new environment for Cryo-EM image processing. Journal of structural biology\| PubMed ID: 16931051	2007
Ligand identification using electron-density map correlations. Acta crystallographica. Section D, Biological crystallography\| PubMed ID: 17164532	2007
Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models. Acta crystallographica. Section D, Biological crystallography\| PubMed ID: 17452785	2007
On macromolecular refinement at subatomic resolution with interatomic scatterers. Acta crystallographica. Section D, Biological crystallography\| PubMed ID: 18007035	2007
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta crystallographica. Section D, Biological crystallography\| PubMed ID: 18094468	2008
Surprises and pitfalls arising from (pseudo)symmetry. Acta crystallographica. Section D, Biological crystallography\| PubMed ID: 18094473	2008
Addressing the need for alternative transportation fuels: the Joint BioEnergy Institute. ACS chemical biology\| PubMed ID: 18205287	2008
A method for the prevention of thrombin-induced degradation of recombinant proteins. Analytical biochemistry\| PubMed ID: 18279654	2008
Protein structures by spallation neutron crystallography. Journal of synchrotron radiation\| PubMed ID: 18421142	2008
Modeling membrane proteins utilizing information from silent amino acid substitutions. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]\| PubMed ID: 18428728	2004
Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias. Acta crystallographica. Section D, Biological crystallography\| PubMed ID: 18453687	2008
Automated structure solution with the PHENIX suite. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 18542881	2008
The protein structure initiative structural genomics knowledgebase. Nucleic acids research\| PubMed ID: 19010965	2009
Crystallographic model quality at a glance. Acta crystallographica. Section D, Biological crystallography\| PubMed ID: 19237753	2009
Phaser crystallographic software. Journal of applied crystallography\| PubMed ID: 19461840	2007
Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules. Acta crystallographica. Section D, Biological crystallography\| PubMed ID: 19465771	2009
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard. Acta crystallographica. Section D, Biological crystallography\| PubMed ID: 19465773	2009
Structure of endoglucanase Cel9A from the thermoacidophilic Alicyclobacillus acidocaldarius. Acta crystallographica. Section D, Biological crystallography\| PubMed ID: 19622857	2009
NMR assignment of Cdc42(T35A), an active Switch I mutant of Cdc42. Biomolecular NMR assignments\| PubMed ID: 19636871	2007
Automatic multiple-zone rigid-body refinement with a large convergence radius. Journal of applied crystallography\| PubMed ID: 19649324	2009
Averaged kick maps: less noise, more signal... and probably less bias. Acta crystallographica. Section D, Biological crystallography\| PubMed ID: 19690370	2009
Recent developments in phasing and structure refinement for macromolecular crystallography. Current opinion in structural biology\| PubMed ID: 19700309	2009
electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation. Acta crystallographica. Section D, Biological crystallography\| PubMed ID: 19770504	2009
A rapid and inexpensive labeling method for microarray gene expression analysis. BMC biotechnology\| PubMed ID: 19939278	2009
On the use of logarithmic scales for analysis of diffraction data. Acta crystallographica. Section D, Biological crystallography\| PubMed ID: 19966414	2009
Robust indexing for automatic data collection. Journal of applied crystallography\| PubMed ID: 20090869	2004
PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta crystallographica. Section D, Biological crystallography\| PubMed ID: 20124702	2010
Crystal structure of the transcriptional activator HlyU from Vibrio vulnificus CMCP6. FEBS letters\| PubMed ID: 20178784	2010
Raman imaging of cell wall polymers in Arabidopsis thaliana. Biochemical and biophysical research communications\| PubMed ID: 20394731	2010
Crystal structures of a group II chaperonin reveal the open and closed states associated with the protein folding cycle. The Journal of biological chemistry\| PubMed ID: 20573955	2010
Biochemical characterization and crystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima. Journal of structural biology\| PubMed ID: 20599513	2010
Molecular simulations provide new insights into the role of the accessory immunoglobulin-like domain of Cel9A. FEBS letters\| PubMed ID: 20609364	2010
phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. Journal of applied crystallography\| PubMed ID: 20648263	2010
A microscale platform for integrated cell-free expression and activity screening of cellulases. Journal of proteome research\| PubMed ID: 20735086	2010
Evidence of functional protein dynamics from X-ray crystallographic ensembles. PLoS computational biology\| PubMed ID: 20865158	2010
High-throughput enzymatic hydrolysis of lignocellulosic biomass via in-situ regeneration. Bioresource technology\| PubMed ID: 20884206	2011
Coupling of receptor conformation and ligand orientation determine graded activity. Nature chemical biology\| PubMed ID: 20924370	2010
Microfluidic glycosyl hydrolase screening for biomass-to-biofuel conversion. Analytical chemistry\| PubMed ID: 20964411	2010
Joint X-ray and neutron refinement with phenix.refine. Acta crystallographica. Section D, Biological crystallography\| PubMed ID: 21041930	2010
Targeted proteomics for metabolic pathway optimization: application to terpene production. Metabolic engineering\| PubMed ID: 21215324	2011
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. Journal of structural and functional genomics\| PubMed ID: 21472436	2011
Exact direct-space asymmetric units for the 230 crystallographic space groups. Acta crystallographica. Section A, Foundations of crystallography\| PubMed ID: 21487185	2011
A switch I mutant of Cdc42 exhibits less conformational freedom. Biochemistry\| PubMed ID: 21667996	2011
The Phenix software for automated determination of macromolecular structures. Methods (San Diego, Calif.)\| PubMed ID: 21821126	2011
Blind image analysis for the compositional and structural characterization of plant cell walls. Analytica chimica acta\| PubMed ID: 21839194	2011
A new generation of crystallographic validation tools for the protein data bank. Structure (London, England : 1993)\| PubMed ID: 22000512	2011
Raman-spectroscopy-based noninvasive microanalysis of native lignin structure. Analytical and bioanalytical chemistry\| PubMed ID: 22071606	2012
Structure of a three-domain sesquiterpene synthase: a prospective target for advanced biofuels production. Structure (London, England : 1993)\| PubMed ID: 22153510	2011
Mechanism of nucleotide sensing in group II chaperonins. The EMBO journal\| PubMed ID: 22193720	2012
iotbx.cif: a comprehensive CIF toolbox. Journal of applied crystallography\| PubMed ID: 22199401	2011
Supplementation of intracellular XylR leads to co-utilization of hemicellulose sugars. Applied and environmental microbiology\| PubMed ID: 22286982	2012
Encoding substrates with mass tags to resolve stereospecific reactions using Nimzyme. Rapid communications in mass spectrometry : RCM\| PubMed ID: 22328213	2012