doi.bio/billy_k_poon

Billy K Poon, PhD

Overview

Billy K Poon is a computational research scientist with expertise in computational biophysics, biochemistry, and biomedical engineering. He has a PhD from Rice University, Houston, TX, and has published extensively in the field of structural biology.

Career

Poon is currently affiliated with the Lawrence Berkeley National Laboratory, where he works on computational crystallographic initiatives.

Notable Publications

Poon has co-authored numerous articles in peer-reviewed journals, including:

Improved AlphaFold modelling with implicit experimental information (Nature Methods). This article describes a method for improving the accuracy of AlphaFold predictions by incorporating experimental data.
CERES: a cryo-EM re-refinement system for continuous improvement of deposited models (Acta Crystallographica, Section D, Structural Biology). This article introduces a system for re-refining cryo-EM models, improving the accuracy of macromolecular structures.
Polder maps: improving OMIT maps by excluding bulk solvent (Acta Crystallographica, Section D, Structural Biology). This publication outlines a method for enhancing OMIT maps, aiding in ligand building and validation.
Three-dimensional single-particle imaging using angular correlations from X-ray laser data (Acta Crystallographica, Section A, Foundations of Crystallography). This article describes a technique for 3D imaging of single particles using X-ray laser data.

- Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-A crystallographic resolution (Proceedings of the National Academy of Sciences of the United States of America). This publication details a method for refining anisotropic thermal parameters of supramolecular complexes.

Billy K Poon

Overview

Billy K Poon, Ph.D., is a computational research scientist specialising in computational biophysics, molecular biophysics, and integrated bioimaging. His research focuses on general biophysics, biochemistry, and biomedical engineering. Poon has contributed to numerous publications in the field of crystallography and structural biology.

Education

Poon received his Ph.D. from Rice University in Houston, Texas.

Career

Poon currently works at the Lawrence Berkeley National Laboratory, where he has co-authored several publications. He is also affiliated with the University of California, Berkeley.

Publications

Poon has an extensive list of publications to his name, with over 25 articles published in prestigious scientific journals. Here are some of his most notable works:

2023: Accelerating crystal structure determination with iterative AlphaFold prediction, co-authored with Terwilliger et al.
2023: Conformational space exploration of cryo-EM structures by variability refinement, co-authored with Afonine et al.
2022: Integration of software tools for integrative modelling of biomolecular systems, co-authored with Hancock et al.
2021: CERES: a cryo-EM re-refinement system for continuous improvement of deposited models, co-authored with Liebschner et al.
2019: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix, co-authored with Liebschner et al.
2018: Free-electron laser data for multiple-particle fluctuation scattering analysis, co-authored with Pande et al.
2013: Three-dimensional single-particle imaging using angular correlations from X-ray laser data, co-authored with Liu et al.
2012: Computation of fluctuation scattering profiles via three-dimensional Zernike polynomials, co-authored with Liu et al.
2010: Autoindexing with outlier rejection and identification of superimposed lattices, co-authored with Sauter.
2007: Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-A crystallographic resolution, co-authored with Poon et al.

Awards and Recognition

Poon has been recognised for his outstanding contributions to the field. He was among the recipients of the 2021 Berkeley Lab Director's Awards, an annual program that acknowledges the exceptional work of employees across all facets of laboratory activities.

Google Scholar

Billy K. Poon

Lawrence Berkeley National Laboratory

https://phenix-online.org/

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=p-a9soAAAAAJ&citationforview=p-a9soAAAAAJ:HtS1dXgVpQUC Cited by: 4463

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=p-a9soAAAAAJ&citationforview=p-a9soAAAAAJ:dBIO0h50nwkC Cited by: 2122

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=p-a9soAAAAAJ&citationforview=p-a9soAAAAAJ:HIFyuExEbWQC 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=p-a9soAAAAAJ&citationforview=p-a9soAAAAAJ:_5tno0g5mFcC Cited by: 596

Shapes and vorticities of superfluid helium nanodroplets LF Gomez, KR Ferguson, JP Cryan, C Bacellar, RMP Tanyag, C Jones, … Science 345 (6199), 906-909, 2014 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=p-a9soAAAAAJ&citationforview=p-a9soAAAAAJ:LkGwnXOMwfcC Cited by: 273

A new method for coarse-grained elastic normal-mode analysis M Lu, B Poon, J Ma Journal of chemical theory and computation 2 (3), 464-471, 2006 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=p-a9soAAAAAJ&citationforview=p-a9soAAAAAJ:u5HHmVD_uO8C Cited by: 105

Improved AlphaFold modeling with implicit experimental information TC Terwilliger, BK Poon, PV Afonine, CJ Schlicksup, TI Croll, C Millán, … Nature methods 19 (11), 1376-1382, 2022 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=p-a9soAAAAAJ&citationforview=p-a9soAAAAAJ:_OXeSy2IsFwC Cited by: 92

AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination TC Terwilliger, D Liebschner, TI Croll, CJ Williams, AJ McCoy, BK Poon, … Nature Methods 21 (1), 110-116, 2024 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=p-a9soAAAAAJ&citationforview=p-a9soAAAAAJ:5MTHONV0fEkC Cited by: 89

Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB) PD Adams, PV Afonine, K Baskaran, HM Berman, J Berrisford, G Bricogne, … Acta Crystallographica Section D: Structural Biology 75 (4), 451-454, 2019 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=p-a9soAAAAAJ&citationforview=p-a9soAAAAAJ:cWzG1nlazyYC Cited by: 63

Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-Å crystallographic resolution BK Poon, X Chen, M Lu, NK Vyas, FA Quiocho, Q Wang, J Ma Proceedings of the National Academy of Sciences 104 (19), 7869-7874, 2007 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=p-a9soAAAAAJ&citationforview=p-a9soAAAAAJ:u-x6o8ySG0sC Cited by: 62

Three-dimensional single-particle imaging using angular correlations from X-ray laser data H Liu, BK Poon, DK Saldin, JCH Spence, PH Zwart Acta Crystallographica Section A: Foundations of Crystallography 69 (4), 365-373, 2013 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=p-a9soAAAAAJ&citationforview=p-a9soAAAAAJ:WF5omc3nYNoC Cited by: 56

Cryofit: Democratization of flexible fitting for cryo-EM DN Kim, NW Moriarty, S Kirmizialtin, PV Afonine, B Poon, OV Sobolev, … Journal of structural biology 208 (1), 1-6, 2019 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=p-a9soAAAAAJ&citationfor_view=p-a9soAAAAAJ:DJbcl8HfkQkC Cited by: 36

Putting AlphaFold models to work with phenix. processpredictedmodel and ISOLDE RD Oeffner, TI Croll, C Millán, BK Poon, CJ Schlicksup, RJ Read, … Acta Crystallographica Section D: Structural Biology 78 (11), 1303-1314, 2022 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=p-a9soAAAAAJ&citationforview=p-a9soAAAAAJ:u-coK7KVo8oC Cited by: 33

Normal-mode refinement of anisotropic thermal parameters for potassium channel KcsA at 3.2 Å crystallographic resolution X Chen, BK Poon, A Dousis, Q Wang, J Ma Structure 15 (8), 955-962, 2007 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=p-a9soAAAAAJ&citationforview=p-a9soAAAAAJ:d1gkVwhDpl0C Cited by: 31

Autoindexing with outlier rejection and identification of superimposed lattices NK Sauter, BK Poon Journal of Applied Crystallography 43 (3), 611-616, 2010 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=p-a9soAAAAAJ&citationforview=p-a9soAAAAAJ:9yKSN-GCB0IC Cited by: 29

Accelerating crystal structure determination with iterative AlphaFold prediction TC Terwilliger, PV Afonine, D Liebschner, TI Croll, AJ McCoy, RD Oeffner, … Acta Crystallographica Section D: Structural Biology 79 (3), 234-244, 2023 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=p-a9soAAAAAJ&citationforview=p-a9soAAAAAJ:fbc8zXXH2BUC Cited by: 28

Structure determination of Pt-coated Au dumbbells via fluctuation X-ray scattering G Chen, MA Modestino, BK Poon, A Schirotzek, S Marchesini, … Journal of synchrotron radiation 19 (5), 695-700, 2012 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=p-a9soAAAAAJ&citationforview=p-a9soAAAAAJ:W7OEmFMy1HYC Cited by: 26

Computation of fluctuation scattering profiles via three-dimensional Zernike polynomials H Liu, BK Poon, AJEM Janssen, PH Zwart Acta Crystallographica Section A: Foundations of Crystallography 68 (5), 561-567, 2012 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=p-a9soAAAAAJ&citationforview=p-a9soAAAAAJ:YsMSGLbcyi4C Cited by: 22

Detection and correction of underassigned rotational symmetry prior to structure deposition BK Poon, RW Grosse-Kunstleve, PH Zwart, NK Sauter Acta Crystallographica Section D: Biological Crystallography 66 (5), 503-513, 2010 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=p-a9soAAAAAJ&citationforview=p-a9soAAAAAJ:qjMakFHDy7sC Cited by: 19

Structural improvement of unliganded simian immunodeficiency virus gp120 core by normal-mode-based X-ray crystallographic refinement X Chen, M Lu, BK Poon, Q Wang, J Ma Acta Crystallographica Section D: Biological Crystallography 65 (4), 339-347, 2009 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=p-a9soAAAAAJ&citationforview=p-a9soAAAAAJ:2osOgNQ5qMEC Cited by: 19

Co-authors

Paul D. Adams googlescholarauthorid pauld.adams.md:K08cxoAAAAJ

Pavel Afonine googlescholarauthorid pavelafonine.md:5OkzCh8AAAAJ

Dorothee Liebschner googlescholarauthorid dorotheeliebschner.md:SfjtO7wAAAAJ

Randy J Read googlescholarauthorid randyj_read.md:BbKCf7UAAAAJ

Tristan Croll googlescholarauthorid tristancroll.md:3oJcpU8AAAAJ

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

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

Christopher J Williams googlescholarauthorid christopherj_williams.md:YMUIF3MAAAAJ

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

Bradley Hintze googlescholarauthorid bradleyhintze.md:rcrjTTcAAAAJ

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

Peter Zwart googlescholarauthorid peterzwart.md:2yUvzdEAAAAJ

Mingyang Lu googlescholarauthorid mingyanglu.md:WgdQw7wAAAAJ

Haiguang Liu googlescholarauthorid haiguangliu.md:O6ZDt9EAAAAJ

Miguel A. Modestino googlescholarauthorid miguela._modestino.md:0zfdancAAAAJ

Fengyun Ni googlescholarauthorid fengyunni.md:DWjME9UAAAAJ

Oliver Gessner googlescholarauthorid olivergessner.md:wTOWE64AAAAJ

James P. Cryan googlescholarauthorid jamesp._cryan.md:ygLoGxIAAAAJ

Erik Malmerberg googlescholarauthorid erikmalmerberg.md:v_Qpl8AAAAAJ

Christoph Bostedt googlescholarauthorid christophbostedt.md:U31p9OgAAAAJ

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