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Author Details

Paul D Adams
Lawrence Berkeley National Laboratory
1994
318
76
Andrej Sali (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
38036854AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination.Nat Methods2024
36762856In situ ligand restraints from quantum-mechanical methods.Acta Crystallogr D Struct Biol2023
37942718Improved joint X-ray and neutron refinement procedure in Phenix.Acta Crystallogr D Struct Biol2023
37724856Simultaneous carbon catabolite repression governs sugar and aromatic co-utilization in <i>Pseudomonas putida</i> M2.Appl Environ Microbiol2023
37057992Expanding Extender Substrate Selection for Unnatural Polyketide Biosynthesis by Acyltransferase Domain Exchange within a Modular Polyketide Synthase.J Am Chem Soc2023
37418444Alkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate format.PLoS One2023
37338214Efficient structure-factor modeling for crystals with multiple components.Acta Crystallogr A Found Adv2023
37138085Structural evidence for intermediates during O<sub>2</sub> formation in photosystem II.Nature2023
37138074Complete integration of carbene-transfer chemistry into biosynthesis.Nature2023
37401915A combinatorial droplet microfluidic device integrated with mass spectrometry for enzyme screening.Lab Chip2023
37431759Overall protein structure quality assessment using hydrogen-bonding parameters.Acta Crystallogr D Struct Biol2023
36849618Structural and biochemical insight into a modular β-1,4-galactan synthase in plants.Nat Plants2023
36811150A Membrane-Associated Light-Harvesting Model is Enabled by Functionalized Assemblies of Gene-Doubled TMV Proteins.Small2023
36876433Accelerating crystal structure determination with iterative AlphaFold prediction.Acta Crystallogr D Struct Biol2023
36435200Rapid quantification of alcohol production in microorganisms based on nanostructure-initiator mass spectrometry (NIMS).Anal Biochem2023
35149213Integration of software tools for integrative modeling of biomolecular systems.J Struct Biol2022
35842458Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease.Sci Rep2022
35505869A Synthetic Gene Library Yields a Previously Unknown Glycoside Phosphorylase That Degrades and Assembles Poly-β-1,3-GlcNAc, Completing the Suite of β-Linked GlcNAc Polysaccharides.ACS Cent Sci2022
35460671PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology.J Mol Biol2022
35359611Scalable and automated CRISPR-based strain engineering using droplet microfluidics.Microsyst Nanoeng2022
36280858Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction.Microbiome2022
36266465Improved AlphaFold modeling with implicit experimental information.Nat Methods2022
35213656Modular automated bottom-up proteomic sample preparation for high-throughput applications.PLoS One2022
33482331Efficient production of oxidized terpenoids via engineering fusion proteins of terpene synthase and cytochrome P450.Metab Eng2021
33825706Protein identification from electron cryomicroscopy maps by automated model building and side-chain matching.Acta Crystallogr D Struct Biol2021
33823127Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality.Structure2021
33542514Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.Nat Methods2021
33926536Experimental and theoretical insights into the effects of pH on catalysis of bond-cleavage by the lignin peroxidase isozyme H8 from Phanerochaete chrysosporium.Biotechnol Biofuels2021
33841364Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology.Front Microbiol2021
33581331Engineering Saccharomyces cerevisiae for isoprenol production.Metab Eng2021
34764256Structural dynamics in the water and proton channels of photosystem II during the S<sub>2</sub> to S<sub>3</sub> transition.Nat Commun2021
34117122Reply to Wang et al.: Clear evidence of binding of Ox to the oxygen-evolving complex of photosystem II is best observed in the omit map.Proc Natl Acad Sci U S A2021
34083602A multiplexed nanostructure-initiator mass spectrometry (NIMS) assay for simultaneously detecting glycosyl hydrolase and lignin modifying enzyme activities.Sci Rep2021
33404525CERES: a cryo-EM re-refinement system for continuous improvement of deposited models.Acta Crystallogr D Struct Biol2021
31599033Cryo-EM map interpretation and protein model-building using iterative map segmentation.Protein Sci2020
31909743Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix.Acta Crystallogr D Struct Biol2020
31793780Structural Mechanism of Regioselectivity in an Unusual Bacterial Acyl-CoA Dehydrogenase.J Am Chem Soc2020
32093835What are the current limits on determination of protonation state using neutron macromolecular crystallography?Methods Enzymol2020
32093832Implementation of the riding hydrogen model in CCTBX to support the next generation of X-ray and neutron joint refinement in Phenix.Methods Enzymol2020
33193240Characterization of a Metal-Resistant <i>Bacillus</i> Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation.Front Microbiol2020
33263321Arginine off-kilter: guanidinium is not as planar as restraints denote.Acta Crystallogr D Struct Biol2020
33122416Draft Genome Sequence of <i>Bacillus</i> sp. Strain EB106-08-02-XG196, Isolated from High-Nitrate-Contaminated Sediment.Microbiol Resour Announc2020
32807957Improvement of cryo-EM maps by density modification.Nat Methods2020
32857966A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry.Structure2020
32868887Novel bacterial clade reveals origin of form I Rubisco.Nat Plants2020
33021493Density modification of cryo-EM maps.Acta Crystallogr D Struct Biol2020
32250597Structure and Function of BorB, the Type II Thioesterase from the Borrelidin Biosynthetic Gene Cluster.Biochemistry2020
32523014An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism.Nat Commun2020
32434915Untangling the sequence of events during the S<sub>2</sub> â¿¿ S<sub>3</sub> transition in photosystem II and implications for the water oxidation mechanism.Proc Natl Acad Sci U S A2020
32160408Response of Pseudomonas putida to Complex, Aromatic-Rich Fractions from Biomass.ChemSusChem2020
  • 1 - 50 of 318

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Collaborators

Thomas C Terwilliger
Los Alamos National Laboratory
Co-authored papers 50
Jay D Keasling
University of California berkeley
Co-authored papers 47
Blake A Simmons
Joint BioEnergy Institute, USA Lawrence Berkeley National Laboratory
Co-authored papers 45
Christopher J Petzold
Joint BioEnergy Institute
Co-authored papers 43
Randy J Read
Cambridge Institute for Medical Research, University of Cambridge
Co-authored papers 35
Trent R Northen
Co-authored papers 22
Edward E K Baidoo
Joint BioEnergy Institute
Co-authored papers 21
Anup K Singh
Joint BioEnergy Institute, USA Lawrence Livermore National Laboratory
Co-authored papers 18
Li-Wei Hung
Los Alamos National Laboratory
Co-authored papers 15
Billy K Poon
Lawrence Berkeley National Laboratory
Co-authored papers 14
Tanveer S Batth
Novo Nordisk Foundation Center for Protein Research, University of Copenhagen
Co-authored papers 12
Steven W Singer
Co-authored papers 12
Aindrila Mukhopadhyay
Joint BioEnergy Institute
Co-authored papers 12
Nathan J Hillson
Lawrence Berkeley National Laboratory
Co-authored papers 12
Helen M Berman
The State University of New Jersey
Co-authored papers 10
Sung-Hou Kim
University of California berkeley
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Rosalind Kim
Lawrence Berkeley National Laboratory
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Adam P Arkin
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John D Westbrook
The State University of New Jersey
Co-authored papers 8
Wah Chiu
Stanford University
Co-authored papers 8
James S Fraser
University of California san francisco
Co-authored papers 8
Terry C Hazen
University of Tennessee
Co-authored papers 7
Brian G Fox
University of Wisconsin-Madison
Co-authored papers 7
Manfred Auer
Southeast University
Co-authored papers 7
Frank DiMaio
University of Washington
Co-authored papers 7
Hector Garcia Martin
Lawrence Berkeley National Laboratory
Co-authored papers 7
Benjamin P Bowen
Co-authored papers 6
Catherine L Lawson
Institute for Quantitative Biomedicine, State University of New Jersey
Co-authored papers 6
Sameer Velankar
European Bioinformatics Institute
Co-authored papers 6
James M Holton
Lawrence Berkeley National Laboratory
Co-authored papers 6
Release 1.2