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D-Index & Metrics

Chemistry

D-Index
101
Citations
176522
World Ranking
1195
National Ranking
468

Research.com Recognitions

  • 1972 - Fellow of American Physical Society (APS)

Overview

Paul D. Adams is affiliated with the Lawrence Berkeley National Laboratory in the United States. Their research primarily focuses on biochemistry, genetics, and molecular biology, with 167 publications contributing to this broad area of study.

Their work spans several subfields, including molecular biology, materials chemistry, biomedical engineering, plant science, and biotechnology. This range illustrates a multidisciplinary approach to scientific inquiry.

Key research topics for Paul D. Adams include:

  • Enzyme Structure and Function
  • Protein Structure and Dynamics
  • Microbial Metabolic Engineering and Bioproduction
  • Advanced Electron Microscopy Techniques and Applications
  • Biofuel production and bioconversion
  • RNA and protein synthesis mechanisms
  • Photosynthetic Processes and Mechanisms

Frequently publishing in several venues, some notable publication venues where Paul D. Adams has contributed include:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • Acta Crystallographica Section D Structural Biology
  • Acta Crystallographica Section A Foundations and Advances
  • Nature Communications
  • Metabolic Engineering

Paul D. Adams has coauthored many papers with several collaborators, including Pavel V. Afonine, Nigel W. Moriarty, J.H. Pereira, Christopher J. Petzold, and Thomas C. Terwilliger. The counts of their collaborations indicate ongoing partnerships in research projects.

Among Paul D. Adams's recent published papers are:

  • "Accurate prediction of protein structures and interactions using a three-track neural network" (2021, Science)
  • "Improvement of cryo-EM maps by density modification" (2020, Nature Methods)
  • "AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination" (2023, Nature Methods)
  • "Untangling the sequence of events during the S 2 → S 3 transition in photosystem II and implications for the water oxidation mechanism" (2020, Proceedings of the National Academy of Sciences)
  • "A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry" (2020, Structure)

Paul D. Adams has been recognized as a Fellow of the American Physical Society (APS) since 1972.

Best Publications

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

    Paul D Adams;Paul D Adams;Pavel Afonine;Gábor Bunkóczi;Vincent B Chen

  • PHENIX: a comprehensive Python-based system for macromolecular structure solution

    Paul D. Adams;Paul D. Adams;Pavel V. Afonine;Gábor Bunkóczi;Vincent B. Chen

  • Phaser crystallographic software

    Airlie J. McCoy;Ralf W. Grosse-Kunstleve;Paul D. Adams;Martyn D. Winn

  • Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

    A.T. Brünger;A.T. Brünger;P.D. Adams;G.M. Clore;W.L. DeLano

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

    D. Liebschner;P.V. Afonine;M.L. Baker;G. Bunkóczi

  • Towards automated crystallographic structure refinement with phenix.refine

    Pavel V. Afonine;Ralf W. Grosse-Kunstleve;Nathaniel Echols;Jeffrey J. Headd

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

    Minkyung Baek;Frank DiMaio;Ivan Anishchenko;Justas Dauparas

  • PHENIX: building new software for automated crystallographic structure determination

    Paul D Adams;Ralf W Grosse-Kunstleve;Li Wei Hung;Thomas R Ioerger

  • MolProbity: More and better reference data for improved all-atom structure validation.

    Christopher J. Williams;Jeffrey J. Headd;Nigel W. Moriarty;Michael G. Prisant

  • Real-space refinement in PHENIX for cryo-EM and crystallography.

    Pavel V. Afonine;Pavel V. Afonine;Billy K. Poon;Randy J. Read;Oleg V. Sobolev

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

    Thomas C Terwilliger;Ralf W Grosse-Kunstleve;Pavel V Afonine;Nigel W Moriarty

  • electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation

    Nigel W. Moriarty;Ralf W. Grosse-Kunstleve;Paul D. Adams;Paul D. Adams

  • Structural basis for double-stranded RNA processing by Dicer.

    Ian J. MacRae;Kaihong Zhou;Fei Li;Adrian Repic

  • The Phenix software for automated determination of macromolecular structures.

    Paul D. Adams;Pavel V. Afonine;Gábor Bunkóczi;Vincent B. Chen

  • Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard

    Thomas C Terwilliger;Paul D Adams;Randy J Read;Airlie J McCoy

  • EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy

    Benjamin A Barad;Nathaniel Echols;Ray Yu-Ruei Wang;Yifan Cheng

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

    Pavel V. Afonine;Pavel V. Afonine;Bruno P. Klaholz;Nigel W. Moriarty;Billy K. Poon

  • Polder maps: improving OMIT maps by excluding bulk solvent.

    Dorothee Liebschner;Pavel V. Afonine;Nigel W. Moriarty;Billy K. Poon

  • Automated Structure Solution with the PHENIX Suite

    Peter H. Zwart;Pavel V. Afonine;Ralf W. Grosse-Kunstleve;Li-Wei Hung

  • Engineering dynamic pathway regulation using stress-response promoters

    Robert H Dahl;Fuzhong Zhang;Jorge Alonso-Gutierrez;Jorge Alonso-Gutierrez;Edward Baidoo;Edward Baidoo

  • Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement

    Paul D. Adams;Navraj S. Pannu;Randy J. Read;Axel T. Brünger

  • iotbx.cif: a comprehensive CIF toolbox.

    Richard J. Gildea;Richard J. Gildea;Luc J. Bourhis;Oleg V. Dolomanov;Ralf W. Grosse-Kunstleve

Frequent Co-Authors

Pavel V. Afonine
Pavel V. Afonine Lawrence Berkeley National Laboratory
Blake A. Simmons
Blake A. Simmons Lawrence Berkeley National Laboratory
Ralf W. Grosse-Kunstleve
Ralf W. Grosse-Kunstleve Lawrence Berkeley National Laboratory
Thomas C. Terwilliger
Thomas C. Terwilliger Los Alamos National Laboratory
Christopher J. Petzold
Christopher J. Petzold Lawrence Berkeley National Laboratory
Jay D. Keasling
Jay D. Keasling University of California, Berkeley
Randy J. Read
Randy J. Read University of Cambridge
Axel T. Brunger
Axel T. Brunger Stanford University
Edward E. K. Baidoo
Edward E. K. Baidoo Lawrence Berkeley National Laboratory
Anup K. Singh
Anup K. Singh Lawrence Livermore National Laboratory

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