doi.bio/paul_d_adams

Paul D Adams

Early Life and Education

Paul D Adams attended Cambridge University (UK) and received a B.A. in Physiology and Pharmacology in 1968. He then continued his education at London University (UK), receiving a Ph.D. in Pharmacology in 1974.

Career

Adams was on the faculty of the University of Texas from 1977 to 1981. He joined the State University of New York at Stony Brook as an Associate Professor of Neurobiology and Behavior in 1981 and was promoted to Professor in 1984. He held concurrent appointments as Professor of Neurology from 1987 to 1989 and Professor of Pharmacological Sciences from 1987 to 2002. Adams was a Howard Hughes Medical Institute Investigator from 1987 to 1995.

Adams currently serves as the Associate Laboratory Director for Biosciences at Berkeley Lab, a position he was appointed to in 2021. He previously served as the interim ALD for the Biosciences Area, taking over for Mary Maxon. Adams has been instrumental in promoting Berkeley Lab's leadership in structural biology on a national and international level.

Research

Adams' research focuses on the development of new algorithms and methods for problems in structural biology. He has collaborated with researchers from Los Alamos National Lab, Duke University, and Cambridge University to develop a new software system called PHENIX, which provides an automated solution for macromolecular structures using crystallographic and cryo-electron microscopy methods. With NIH funding, the scope of PHENIX has been expanded to include the analysis of neutron diffraction data.

Adams is also involved in bioenergy research, working on the development of new technologies to improve the conversion of biomass to fuels as part of the Joint Bioenergy Institute. He has also contributed to the chemical imaging of plant cell wall material and the structural study of large macromolecular machines.

Awards and Recognition

Novartis Memorial Prize (1979, British Pharmacological Society)
Gaddum Memorial Award (1984, British Pharmacological Society)
MacArthur Foundation Prize Fellow (1986)
Fellow of the Royal Society (elected 1991)

Selected Publications

Adams, P.R. and Cox, K.J.A. (2002). Synaptic Darwinism and neocortical function. Neurocomputing 42, 197-214
Cox, K.J.A. and Adams, P.R. (2000). Implications of synaptic digitisation and error for neocortical function. Neurocomputing. 32-33, 673-678
Adams P. (2000) To Sleep, Perchance to Dream. Science Spectra 23, 46-55
Adams, P.R (1998). Hebb and Darwin. J. Theoret. Biol. 195:419-438

- Zhou,Q., Godwin,D.W., O'Malley,D.M. and Adams, P.R. (1997). Visualisation of calcium influx through channels that shape the burst and tonic firing modes of thalamic relay cells. J. Neurophysiol. 77: 2816-2825

Paul D Adams

Overview

Paul D Adams is a neuroscientist and professor in the Department of Neurobiology and Behavior at Stony Brook University in New York. He has previously served as a researcher at the University of Edinburgh and the University of California, Berkeley, and is currently Associate Laboratory Director for Biosciences at Lawrence Berkeley National Laboratory. Adams' research focuses on the development of new algorithms and methods for structural biology problems, bioenergy research, and the study of large macromolecular machines.

Education

Adams attended Cambridge University, where he received a B.A. in Physiology and Pharmacology in 1968. He then pursued a Ph.D. in Pharmacology at London University, graduating in 1974.

Career

Adams began his career as a faculty member at the University of Texas from 1977 to 1981. He then joined the State University of New York at Stony Brook as an Associate Professor of Neurobiology and Behavior in 1981 and was promoted to Professor in 1984. During this time, he also held concurrent appointments as Professor of Neurology (1987-1989) and Professor of Pharmacological Sciences (1987-2002). From 1987 to 1995, Adams was an investigator at the Howard Hughes Medical Institute.

Awards and Recognition

Adams has received numerous awards and recognition for his work. He was awarded the Novartis Memorial Prize in 1979 and the Gaddum Memorial Award in 1984, both from the British Pharmacological Society. He was also a recipient of the MacArthur Foundation Prize in 1986 and was elected a Fellow of the Royal Society in 1991.

Research and Publications

Adams has made significant contributions to the fields of neuroscience and structural biology. He pioneered the concepts of open-channel block and neuromodulation, which are now central to neuroscience. He has also proposed the theory of "Hebbian proofreading" to address the challenges of synaptic adjustments in the neocortex.

Adams has published extensively in his field. Some of his notable publications include:

Adams, P.R. and Cox, K.J.A. (2002). Synaptic Darwinism and neocortical function. Neurocomputing 42, 197-214
Cox, K.J.A. and Adams, P.R. (2000). Implications of synaptic digitisation and error for neocortical function. Neurocomputing. 32-33, 673-678
Adams, P and Cox, K. (2006). A neurobiological perspective on building intelligent devices. The Neuromorphic Engineer 3, 2-10
Adams, P.R (1998). Hebb and Darwin. J. Theoret. Biol. 195:419-438
Zhou,Q., Godwin,D.W., O'Malley,D.M. and Adams, P.R. (1997). Visualisation of calcium influx through channels that shape the burst and tonic firing modes of thalamic relay cells. J. Neurophysiol. 77: 2816-2825

Google Scholar Profile

Paul D Adams)

Google Scholar

Paul D. Adams Lawrence Berkeley Laboratory & University of California Berkeley http://cci.lbl.gov/paul/ PHENIX: a comprehensive Python-based system for macromolecular structure solution PD Adams, PV Afonine, G Bunkóczi, VB Chen, IW Davis, N Echols, … Acta Crystallographica Section D: Biological Crystallography 66 (2), 213-221, 2010 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=K08cxoAAAAJ&citationforview=K08cxoAAAAJ:9yKSN-GCB0IC Cited by: 23602

Phaser crystallographic software AJ McCoy, RW Grosse-Kunstleve, PD Adams, MD Winn, LC Storoni, … Journal of applied crystallography 40 (4), 658-674, 2007 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=K08cxoAAAAJ&citationforview=K08cxoAAAAJ:mgoTDWlsYNUC Cited by: 20850

Crystallography & NMR system: A new software suite for macromolecular structure determination AT Brünger, PD Adams, GM Clore, WL DeLano, P Gros, … Biological Crystallography 54 (5), 905-921, 1998 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=K08cxoAAAAJ&citationforview=K08cxoAAAAJ:bKqednn6t2AC Cited by: 20659

Towards automated crystallographic structure refinement with phenix. refine PV Afonine, RW Grosse-Kunstleve, N Echols, JJ Headd, NW Moriarty, … Acta Crystallographica Section D: Biological Crystallography 68 (4), 352-367, 2012 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=K08cxoAAAAJ&citationforview=K08cxoAAAAJ:2KloaMYe4IUC Cited by: 5226

PHENIX: building new software for automated crystallographic structure determination PD Adams, RW Grosse-Kunstleve, LW Hung, TR Ioerger, AJ McCoy, … Acta Crystallographica Section D: Biological Crystallography 58 (11), 1948-1954, 2002 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=K08cxoAAAAJ&citationforview=K08cxoAAAAJ:d1gkVwhDpl0C Cited by: 4859

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix D Liebschner, PV Afonine, ML Baker, G Bunkóczi, VB Chen, TI Croll, … Acta Crystallographica Section D: Structural Biology 75 (10), 861-877, 2019 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=K08cxoAAAAJ&citationforview=K08cxoAAAAJ:3vbIHxFL9FgC Cited by: 4462

Accurate prediction of protein structures and interactions using a three-track neural network M Baek, F DiMaio, I Anishchenko, J Dauparas, S Ovchinnikov, GR Lee, … Science 373 (6557), 871-876, 2021 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=K08cxoAAAAJ&citationforview=K08cxoAAAAJ:hEXC_dOfxuUC Cited by: 3649

MolProbity: more and better reference data for improved all‐atom structure validation CJ Williams, JJ Headd, NW Moriarty, MG Prisant, LL Videau, LN Deis, … Protein Science 27 (1), 293-315, 2018 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=K08cxoAAAAJ&citationforview=K08cxoAAAAJ:M0leSnx2MbUC Cited by: 3050

Real-space refinement in PHENIX for cryo-EM and crystallography PV Afonine, BK Poon, RJ Read, OV Sobolev, TC Terwilliger, … Acta Crystallographica Section D: Structural Biology 74 (6), 531-544, 2018 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=K08cxoAAAAJ&citationforview=K08cxoAAAAJ:ifOnle78iJkC Cited by: 2123

Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard TC Terwilliger, RW Grosse-Kunstleve, PV Afonine, NW Moriarty, PH Zwart, … Acta Crystallographica Section D: Biological Crystallography 64 (1), 61-69, 2008 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=K08cxoAAAAJ&citationforview=K08cxoAAAAJ:hqOjcs7Dif8C Cited by: 1613

Structural basis for double-stranded RNA processing by Dicer IJ MacRae, K Zhou, F Li, A Repic, AN Brooks, WZ Cande, PD Adams, … Science 311 (5758), 195-198, 2006 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=K08cxoAAAAJ&citationforview=K08cxoAAAAJ:qjMakFHDy7sC Cited by: 1314

electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation NW Moriarty, RW Grosse-Kunstleve, PD Adams Acta Crystallographica Section D: Biological Crystallography 65 (10), 1074-1080, 2009 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=K08cxoAAAAJ&citationforview=K08cxoAAAAJ:L8Ckcad2t8MC Cited by: 1235

Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard TC Terwilliger, PD Adams, RJ Read, AJ McCoy, NW Moriarty, … Acta Crystallographica Section D: Biological Crystallography 65 (6), 582-601, 2009 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=K08cxoAAAAJ&citationforview=K08cxoAAAAJ:hFOr9nPyWt4C Cited by: 921

The Phenix software for automated determination of macromolecular structures PD Adams, PV Afonine, G Bunkóczi, VB Chen, N Echols, JJ Headd, … Methods 55 (1), 94-106, 2011 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=K08cxoAAAAJ&citationforview=K08cxoAAAAJ:mvPsJ3kp5DgC Cited by: 854

EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy BA Barad, N Echols, RYR Wang, Y Cheng, F DiMaio, PD Adams, … Nature methods 12 (10), 943-946, 2015 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=K08cxoAAAAJ&citationforview=K08cxoAAAAJ:UuEBAcK4md4C Cited by: 752

New tools for the analysis and validation of cryo-EM maps and atomic models PV Afonine, BP Klaholz, NW Moriarty, BK Poon, OV Sobolev, … Acta Crystallographica Section D: Structural Biology 74 (9), 814-840, 2018 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=K08cxoAAAAJ&citationforview=K08cxoAAAAJ:6ZzL7HXColQC Cited by: 600

Polder maps: improving OMIT maps by excluding bulk solvent D Liebschner, PV Afonine, NW Moriarty, BK Poon, OV Sobolev, … Acta Crystallographica Section D: Structural Biology 73 (2), 148-157, 2017 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=K08cxoAAAAJ&citationforview=K08cxoAAAAJ:RuPIJ_LgqDgC Cited by: 596

Automated structure solution with the PHENIX suite PH Zwart, PV Afonine, RW Grosse-Kunstleve, LW Hung, TR Ioerger, … Structural proteomics: high-throughput methods, 419-435, 2008 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=K08cxoAAAAJ&citationforview=K08cxoAAAAJ:WF5omc3nYNoC Cited by: 582

Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement PD Adams, NS Pannu, RJ Read, AT Brünger Proceedings of the National Academy of Sciences 94 (10), 5018-5023, 1997 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=K08cxoAAAAJ&citationforview=K08cxoAAAAJ:2osOgNQ5qMEC Cited by: 525

Engineering dynamic pathway regulation using stress-response promoters RH Dahl, F Zhang, J Alonso-Gutierrez, E Baidoo, TS Batth, … Nature biotechnology 31 (11), 1039-1046, 2013 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=K08cxoAAAAJ&citationforview=K08cxoAAAAJ:uDGL6kOW6j0C Cited by: 520

Co-authors

Pavel Afonine 5OkzCh8AAAAJ

Randy J Read BbKCf7UAAAAJ

Axel Brunger fXsieHkAAAAJ

Dr Airlie J. McCoy vdDwlucAAAAJ

Peter Zwart 2yUvzdEAAAAJ

Li-Wei Hung ThQIKZMAAAAJ

Jane S. Richardson UF1_VRcAAAAJ

Jay Keasling MO3BwFMAAAAJ

Jeff Headd UrL7Cv4AAAAJ

David C. Richardson 7P3t1woAAAAJ

Blake A. Simmons c-RPud4AAAAJ

Sacha Urzhumtsev vY3DbUUAAAAJ

Christopher J Petzold 0JsOgl0AAAAJ

Luke Rice NLb7x2sAAAAJ

Billy K. Poon p-a9soAAAAAJ

Dorothee Liebschner SfjtO7wAAAAJ

Piet Gros fYwKExoAAAAJ

Jose Henrique Pereira 2ckIxEMAAAAJ

Ian W. Davis gDtFWBIAAAAJ

Taek Soon Lee l-1_1ucAAAAJ

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Co-authors

Pavel Afonine googlescholarauthor_id:5OkzCh8AAAAJ

Randy J Read googlescholarauthor_id:BbKCf7UAAAAJ

Axel Brunger googlescholarauthor_id:fXsieHkAAAAJ

Dr Airlie J. McCoy googlescholarauthor_id:vdDwlucAAAAJ

Peter Zwart googlescholarauthor_id:2yUvzdEAAAAJ

Li-Wei Hung googlescholarauthor_id:ThQIKZMAAAAJ

Jane S. Richardson googlescholarauthorid:UF1VRcAAAAJ

Jay Keasling googlescholarauthor_id:MO3BwFMAAAAJ

Jeff Headd googlescholarauthor_id:UrL7Cv4AAAAJ

David C. Richardson googlescholarauthor_id:7P3t1woAAAAJ

Blake A. Simmons googlescholarauthor_id:c-RPud4AAAAJ

Sacha Urzhumtsev googlescholarauthor_id:vY3DbUUAAAAJ

Christopher J Petzold googlescholarauthor_id:0JsOgl0AAAAJ

Luke Rice googlescholarauthor_id:NLb7x2sAAAAJ

Billy K. Poon googlescholarauthor_id:p-a9soAAAAAJ

Dorothee Liebschner googlescholarauthor_id:SfjtO7wAAAAJ

Piet Gros googlescholarauthor_id:fYwKExoAAAAJ

Jose Henrique Pereira googlescholarauthor_id:2ckIxEMAAAAJ

Ian W. Davis googlescholarauthor_id:gDtFWBIAAAAJ

Taek Soon Lee googlescholarauthorid:l-11ucAAAAJ

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Co-authors

Pavel Afonine googlescholarauthorid pavelafonine.md:5OkzCh8AAAAJ

Randy J Read googlescholarauthorid randyj_read.md:BbKCf7UAAAAJ

Axel Brunger googlescholarauthorid axelbrunger.md:fXsieHkAAAAJ

Dr Airlie J. McCoy googlescholarauthorid drairliej.mccoy.md:vdDwlucAAAAJ

Peter Zwart googlescholarauthorid peterzwart.md:2yUvzdEAAAAJ

Li-Wei Hung googlescholarauthorid li-weihung.md:ThQIKZMAAAAJ

Jane S. Richardson googlescholarauthorid janes.richardson.md:UF1VRcAAAAJ

Jay Keasling googlescholarauthorid jaykeasling.md:MO3BwFMAAAAJ

Jeff Headd googlescholarauthorid jeffheadd.md:UrL7Cv4AAAAJ

David C. Richardson googlescholarauthorid davidc._richardson.md:7P3t1woAAAAJ

Blake A. Simmons googlescholarauthorid blakea._simmons.md:c-RPud4AAAAJ

Sacha Urzhumtsev googlescholarauthorid sachaurzhumtsev.md:vY3DbUUAAAAJ

Christopher J Petzold googlescholarauthorid christopherj_petzold.md:0JsOgl0AAAAJ

Luke Rice googlescholarauthorid lukerice.md:NLb7x2sAAAAJ

Billy K. Poon googlescholarauthorid billyk._poon.md:p-a9soAAAAAJ

Dorothee Liebschner googlescholarauthorid dorotheeliebschner.md:SfjtO7wAAAAJ

Piet Gros googlescholarauthorid pietgros.md:fYwKExoAAAAJ

Jose Henrique Pereira googlescholarauthorid josehenrique_pereira.md:2ckIxEMAAAAJ

Ian W. Davis googlescholarauthorid ianw._davis.md:gDtFWBIAAAAJ

Taek Soon Lee googlescholarauthorid taeksoonlee.md:l-11ucAAAAJ

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Paul D. Adams

Lawrence Berkeley Laboratory & University of California Berkeley

http://cci.lbl.gov/paul/

PHENIX: a comprehensive Python-based system for macromolecular structure solution PD Adams, PV Afonine, G Bunkóczi, VB Chen, IW Davis, N Echols, … Acta Crystallographica Section D: Biological Crystallography 66 (2), 213-221, 2010 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=K08cxoAAAAJ&citationforview=K08cxoAAAAJ:9yKSN-GCB0IC