Paul D. Adams Physical Biosciences Division Lawrence Berkeley National Laboratory Biography Publications Institution JoVE Articles Paul D. Adams has not added a biography. If you are Paul D. Adams and would like to personalize this page please email our Author Liaison for assistance. Publications Encoding Substrates with Mass Tags to Resolve Stereospecific Reactions Using Nimzyme Rapid Communications in Mass Spectrometry : RCM. Mar, 2012 | Pubmed ID: 22328213 Supplementation of Intracellular XylR Leads to Co-utilization of Hemicellulose Sugars Applied and Environmental Microbiology. Jan, 2012 | Pubmed ID: 22286982 Mechanism of Nucleotide Sensing in Group II Chaperonins The EMBO Journal. Feb, 2012 | Pubmed ID: 22193720 Raman-spectroscopy-based Noninvasive Microanalysis of Native Lignin Structure Analytical and Bioanalytical Chemistry. Jan, 2012 | Pubmed ID: 22071606 Iotbx.cif: a Comprehensive CIF Toolbox Journal of Applied Crystallography. Dec, 2011 | Pubmed ID: 22199401 Structure of a Three-domain Sesquiterpene Synthase: a Prospective Target for Advanced Biofuels Production Structure (London, England : 1993). Dec, 2011 | Pubmed ID: 22153510 A New Generation of Crystallographic Validation Tools for the Protein Data Bank Structure (London, England : 1993). Oct, 2011 | Pubmed ID: 22000512 Blind Image Analysis for the Compositional and Structural Characterization of Plant Cell Walls Analytica Chimica Acta. Sep, 2011 | Pubmed ID: 21839194 The Phenix Software for Automated Determination of Macromolecular Structures Methods (San Diego, Calif.). Sep, 2011 | Pubmed ID: 21821126 A Switch I Mutant of Cdc42 Exhibits Less Conformational Freedom Biochemistry. Jul, 2011 | Pubmed ID: 21667996 Exact Direct-space Asymmetric Units for the 230 Crystallographic Space Groups Acta Crystallographica. Section A, Foundations of Crystallography. May, 2011 | Pubmed ID: 21487185 The Structural Biology Knowledgebase: a Portal to Protein Structures, Sequences, Functions, and Methods Journal of Structural and Functional Genomics. Jul, 2011 | Pubmed ID: 21472436 Targeted Proteomics for Metabolic Pathway Optimization: Application to Terpene Production Metabolic Engineering. Mar, 2011 | Pubmed ID: 21215324 High-throughput Enzymatic Hydrolysis of Lignocellulosic Biomass Via In-situ Regeneration Bioresource Technology. Jan, 2011 | Pubmed ID: 20884206 Joint X-ray and Neutron Refinement with Phenix.refine Acta Crystallographica. Section D, Biological Crystallography. Nov, 2010 | Pubmed ID: 21041930 Microfluidic Glycosyl Hydrolase Screening for Biomass-to-biofuel Conversion Analytical Chemistry. Nov, 2010 | Pubmed ID: 20964411 Coupling of Receptor Conformation and Ligand Orientation Determine Graded Activity Nature Chemical Biology. Nov, 2010 | Pubmed ID: 20924370 Evidence of Functional Protein Dynamics from X-ray Crystallographic Ensembles PLoS Computational Biology. 2010 | Pubmed ID: 20865158 A Microscale Platform for Integrated Cell-free Expression and Activity Screening of Cellulases Journal of Proteome Research. Nov, 2010 | Pubmed ID: 20735086 Phenix.model_vs_data: a High-level Tool for the Calculation of Crystallographic Model and Data Statistics Journal of Applied Crystallography. Aug, 2010 | Pubmed ID: 20648263 Molecular Simulations Provide New Insights into the Role of the Accessory Immunoglobulin-like Domain of Cel9A FEBS Letters. Aug, 2010 | Pubmed ID: 20609364 Biochemical Characterization and Crystal Structure of Endoglucanase Cel5A from the Hyperthermophilic Thermotoga Maritima Journal of Structural Biology. Dec, 2010 | Pubmed ID: 20599513 Crystal Structures of a Group II Chaperonin Reveal the Open and Closed States Associated with the Protein Folding Cycle The Journal of Biological Chemistry. Sep, 2010 | Pubmed ID: 20573955 Raman Imaging of Cell Wall Polymers in Arabidopsis Thaliana Biochemical and Biophysical Research Communications. May, 2010 | Pubmed ID: 20394731 Crystal Structure of the Transcriptional Activator HlyU from Vibrio Vulnificus CMCP6 FEBS Letters. Mar, 2010 | Pubmed ID: 20178784 PHENIX: a Comprehensive Python-based System for Macromolecular Structure Solution Acta Crystallographica. Section D, Biological Crystallography. Feb, 2010 | Pubmed ID: 20124702 On the Use of Logarithmic Scales for Analysis of Diffraction Data Acta Crystallographica. Section D, Biological Crystallography. Dec, 2009 | Pubmed ID: 19966414 A Rapid and Inexpensive Labeling Method for Microarray Gene Expression Analysis BMC Biotechnology. 2009 | Pubmed ID: 19939278 Electronic Ligand Builder and Optimization Workbench (eLBOW): a Tool for Ligand Coordinate and Restraint Generation Acta Crystallographica. Section D, Biological Crystallography. Oct, 2009 | Pubmed ID: 19770504 Recent Developments in Phasing and Structure Refinement for Macromolecular Crystallography Current Opinion in Structural Biology. Oct, 2009 | Pubmed ID: 19700309 Averaged Kick Maps: Less Noise, More Signal... and Probably Less Bias Acta Crystallographica. Section D, Biological Crystallography. Sep, 2009 | Pubmed ID: 19690370 Automatic Multiple-zone Rigid-body Refinement with a Large Convergence Radius Journal of Applied Crystallography. Aug, 2009 | Pubmed ID: 19649324 Structure of Endoglucanase Cel9A from the Thermoacidophilic Alicyclobacillus Acidocaldarius Acta Crystallographica. Section D, Biological Crystallography. Aug, 2009 | Pubmed ID: 19622857 Decision-making in Structure Solution Using Bayesian Estimates of Map Quality: the PHENIX AutoSol Wizard Acta Crystallographica. Section D, Biological Crystallography. Jun, 2009 | Pubmed ID: 19465773 Generalized X-ray and Neutron Crystallographic Analysis: More Accurate and Complete Structures for Biological Macromolecules Acta Crystallographica. Section D, Biological Crystallography. Jun, 2009 | Pubmed ID: 19465771 Crystallographic Model Quality at a Glance Acta Crystallographica. Section D, Biological Crystallography. Mar, 2009 | Pubmed ID: 19237753 The Protein Structure Initiative Structural Genomics Knowledgebase Nucleic Acids Research. Jan, 2009 | Pubmed ID: 19010965 Automated Structure Solution with the PHENIX Suite Methods in Molecular Biology (Clifton, N.J.). 2008 | Pubmed ID: 18542881 Iterative-build OMIT Maps: Map Improvement by Iterative Model Building and Refinement Without Model Bias Acta Crystallographica. Section D, Biological Crystallography. May, 2008 | Pubmed ID: 18453687 Protein Structures by Spallation Neutron Crystallography Journal of Synchrotron Radiation. May, 2008 | Pubmed ID: 18421142 A Method for the Prevention of Thrombin-induced Degradation of Recombinant Proteins Analytical Biochemistry. Apr, 2008 | Pubmed ID: 18279654 Addressing the Need for Alternative Transportation Fuels: the Joint BioEnergy Institute ACS Chemical Biology. Jan, 2008 | Pubmed ID: 18205287 Surprises and Pitfalls Arising from (pseudo)symmetry Acta Crystallographica. Section D, Biological Crystallography. Jan, 2008 | Pubmed ID: 18094473 Iterative Model Building, Structure Refinement and Density Modification with the PHENIX AutoBuild Wizard Acta Crystallographica. Section D, Biological Crystallography. Jan, 2008 | Pubmed ID: 18094468 NMR Assignment of Cdc42(T35A), an Active Switch I Mutant of Cdc42 Biomolecular NMR Assignments. Dec, 2007 | Pubmed ID: 19636871 Phaser Crystallographic Software Journal of Applied Crystallography. Aug, 2007 | Pubmed ID: 19461840 On Macromolecular Refinement at Subatomic Resolution with Interatomic Scatterers Acta Crystallographica. Section D, Biological Crystallography. Nov, 2007 | Pubmed ID: 18007035 Interpretation of Ensembles Created by Multiple Iterative Rebuilding of Macromolecular Models Acta Crystallographica. Section D, Biological Crystallography. May, 2007 | Pubmed ID: 17452785 Ligand Identification Using Electron-density Map Correlations Acta Crystallographica. Section D, Biological Crystallography. Jan, 2007 | Pubmed ID: 17164532 SPARX, a New Environment for Cryo-EM Image Processing Journal of Structural Biology. Jan, 2007 | Pubmed ID: 16931051 Automated Ligand Fitting by Core-fragment Fitting and Extension into Density Acta Crystallographica. Section D, Biological Crystallography. Aug, 2006 | Pubmed ID: 16855309 Solution Structure of an Oncogenic Mutant of Cdc42Hs Biochemistry. Feb, 2006 | Pubmed ID: 16489751 Structural Basis for Double-stranded RNA Processing by Dicer Science (New York, N.Y.). Jan, 2006 | Pubmed ID: 16410517 Crystal Structures of an NAD Kinase from Archaeoglobus Fulgidus in Complex with ATP, NAD, or NADP Journal of Molecular Biology. Nov, 2005 | Pubmed ID: 16242716 Structural Genomics of Minimal Organisms and Protein Fold Space Journal of Structural and Functional Genomics. 2005 | Pubmed ID: 16211501 Automated Crystallographic Ligand Building Using the Medial Axis Transform of an Electron-density Isosurface Acta Crystallographica. Section D, Biological Crystallography. Oct, 2005 | Pubmed ID: 16204887 Crystal Structure of a Bacterial Ribonuclease P RNA Proceedings of the National Academy of Sciences of the United States of America. Sep, 2005 | Pubmed ID: 16157868 A Robust Bulk-solvent Correction and Anisotropic Scaling Procedure Acta Crystallographica. Section D, Biological Crystallography. Jul, 2005 | Pubmed ID: 15983406 Crystal Structure of a Heat-inducible Transcriptional Repressor HrcA from Thermotoga Maritima: Structural Insight into DNA Binding and Dimerization Journal of Molecular Biology. Jul, 2005 | Pubmed ID: 15979091 Crystal Structure of the "PhoU-like" Phosphate Uptake Regulator from Aquifex Aeolicus Journal of Bacteriology. Jun, 2005 | Pubmed ID: 15937186 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. Mar, 2005 | Pubmed ID: 15728358 Crystal Structure of a PhoU Protein Homologue: a New Class of Metalloprotein Containing Multinuclear Iron Clusters The Journal of Biological Chemistry. Apr, 2005 | Pubmed ID: 15716271 Robust Indexing for Automatic Data Collection Journal of Applied Crystallography. Jun, 2004 | Pubmed ID: 20090869 Modeling Membrane Proteins Utilizing Information from Silent Amino Acid Substitutions Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [et Al.]. Feb, 2004 | Pubmed ID: 18428728 Exploring the Structural Dynamics of the E.coli Chaperonin GroEL Using Translation-libration-screw Crystallographic Refinement of Intermediate States Journal of Molecular Biology. Sep, 2004 | Pubmed ID: 15313620 Backbone Dynamics of an Oncogenic Mutant of Cdc42Hs Shows Increased Flexibility at the Nucleotide-binding Site Biochemistry. Aug, 2004 | Pubmed ID: 15287724 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. Jan, 2004 | Pubmed ID: 14659753 Recent Developments in the PHENIX Software for Automated Crystallographic Structure Determination Journal of Synchrotron Radiation. Jan, 2004 | Pubmed ID: 14646133 Automatic Solution of Heavy-atom Substructures Methods in Enzymology. 2003 | Pubmed ID: 14696368 Role of the Gamma-phosphate of ATP in Triggering Protein Folding by GroEL-GroES: Function, Structure and Energetics The EMBO Journal. Oct, 2003 | Pubmed ID: 14517228 X-ray Crystallographic and Kinetic Studies of Human Sorbitol Dehydrogenase Structure (London, England : 1993). Sep, 2003 | Pubmed ID: 12962626 High-resolution Structure of RNase P Protein from Thermotoga Maritima Proceedings of the National Academy of Sciences of the United States of America. Jun, 2003 | Pubmed ID: 12799461 Computational Aspects of High-throughput Crystallographic Macromolecular Structure Determination Methods of Biochemical Analysis. 2003 | Pubmed ID: 12647382 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. Nov, 2002 | Pubmed ID: 12405862 PHENIX: Building New Software for Automated Crystallographic Structure Determination Acta Crystallographica. Section D, Biological Crystallography. Nov, 2002 | Pubmed ID: 12393927 Intramolecular Quenching of Tryptophan Fluorescence by the Peptide Bond in Cyclic Hexapeptides Journal of the American Chemical Society. Aug, 2002 | Pubmed ID: 12149035 Protein Science : a Publication of the Protein Society. Jul, 2002 | Pubmed ID: 12070332 Molecular Dynamics Applied to X-ray Structure Refinement Accounts of Chemical Research. Jun, 2002 | Pubmed ID: 12069625 Label-free in situ Imaging of Lignification in Plant Cell Walls Martin Schmidt1, Pradeep Perera1, Adam M. Schwartzberg2, Paul D. Adams3, P. James Schuck2 1Energy Biosciences Institute, University of California, Berkeley, 2Molecular Foundry, Lawrence Berkeley National Laboratory, 3Physical Biosciences Division, Lawrence Berkeley National Laboratory JoVE 2064 Biology
Label-free in situ Imaging of Lignification in Plant Cell Walls Martin Schmidt1, Pradeep Perera1, Adam M. Schwartzberg2, Paul D. Adams3, P. James Schuck2 1Energy Biosciences Institute, University of California, Berkeley, 2Molecular Foundry, Lawrence Berkeley National Laboratory, 3Physical Biosciences Division, Lawrence Berkeley National Laboratory JoVE 2064 Biology
