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Ben Hall

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InstitutionUniversity of Chicago
AddressChicago IL 60637
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Zerrouk N, Alcraft R, Hall BA, Augé F, Niarakis A. Large-scale computational modelling of the M1 and M2 synovial macrophages in rheumatoid arthritis. NPJ Syst Biol Appl. 2024 Jan 26; 10(1):10. PMID: 38272919; PMCID: PMC10811231.
      Citations:    Fields:    Translation:HumansCells
    2. Jamshidi Parvar S, Hall BA, Shorthouse D. Interpreting the effect of mutations to protein binding sites from large-scale genomic screens. Methods. 2024 Feb; 222:122-132. PMID: 38185227.
      Citations:    Fields:    Translation:Cells
    3. Shorthouse D, Zhuang L, Rahrmann EP, Kosmidou C, Wickham Rahrmann K, Hall M, Greenwood B, Devonshire G, Gilbertson RJ, Fitzgerald RC, Hall BA. KCNQ potassium channels modulate Wnt activity in gastro-oesophageal adenocarcinomas. Life Sci Alliance. 2023 12; 6(12). PMID: 37748809; PMCID: PMC10520261.
      Citations: 1     Fields:    Translation:Humans
    4. King C, Fowler JC, Abnizova I, Sood RK, Hall MWJ, Szeverényi I, Tham M, Huang J, Young SM, Hall BA, Birgitte Lane E, Jones PH. Author Correction: Somatic mutations in facial skin from countries of contrasting skin cancer risk. Nat Genet. 2023 Sep; 55(9):1608. PMID: 37626225; PMCID: PMC10484781.
      Citations: 1     Fields:    
    5. Foley K, Shorthouse D, Rahrmann E, Zhuang L, Devonshire G, Gilbertson RJ, OCCAMS consortium, Fitzgerald RC, Hall BA. SMAD4 and KCNQ3 alterations are associated with lymph node metastases in oesophageal adenocarcinoma. Biochim Biophys Acta Mol Basis Dis. 2024 01; 1870(1):166867. PMID: 37648039.
      Citations:    Fields:    Translation:Humans
    6. King C, Fowler JC, Abnizova I, Sood RK, Hall MWJ, Szeverényi I, Tham M, Huang J, Young SM, Hall BA, Birgitte Lane E, Jones PH. Somatic mutations in facial skin from countries of contrasting skin cancer risk. Nat Genet. 2023 09; 55(9):1440-1447. PMID: 37537257; PMCID: PMC10484783.
      Citations: 1     Fields:    Translation:HumansCells
    7. Hall MWJ, Shorthouse D, Alcraft R, Jones PH, Hall BA. Mutations observed in somatic evolution reveal underlying gene mechanisms. Commun Biol. 2023 07 19; 6(1):753. PMID: 37468606; PMCID: PMC10356810.
      Citations:    
    8. Abby E, Dentro SC, Hall MWJ, Fowler JC, Ong SH, Sood R, Herms A, Piedrafita G, Abnizova I, Siebel CW, Gerstung M, Hall BA, Jones PH. Notch1 mutations drive clonal expansion in normal esophageal epithelium but impair tumor growth. Nat Genet. 2023 02; 55(2):232-245. PMID: 36658434; PMCID: PMC9925379.
      Citations: 11     Fields:    Translation:HumansAnimals
    9. Shorthouse D, Bradley J, Critchlow SE, Bendtsen C, Hall BA. Heterogeneity of the cancer cell line metabolic landscape. Mol Syst Biol. 2022 11; 18(11):e11006. PMID: 36321551; PMCID: PMC9627668.
      Citations: 4     Fields:    Translation:HumansCells
    10. Murai K, Dentro S, Ong SH, Sood R, Fernandez-Antoran D, Herms A, Kostiou V, Abnizova I, Hall BA, Gerstung M, Jones PH. p53 mutation in normal esophagus promotes multiple stages of carcinogenesis but is constrained by clonal competition. Nat Commun. 2022 10 20; 13(1):6206. PMID: 36266286; PMCID: PMC9584949.
      Citations: 6     Fields:    Translation:HumansAnimalsCells
    11. Talarmain L, Clarke MA, Shorthouse D, Cabrera-Cosme L, Kent DG, Fisher J, Hall BA. HOXA9 has the hallmarks of a biological switch with implications in blood cancers. Nat Commun. 2022 10 03; 13(1):5829. PMID: 36192425; PMCID: PMC9530117.
      Citations: 3     Fields:    Translation:Humans
    12. Rahrmann EP, Shorthouse D, Jassim A, Hu LP, Ortiz M, Mahler-Araujo B, Vogel P, Paez-Ribes M, Fatemi A, Hannon GJ, Iyer R, Blundon JA, Kay J, Nazarian RM, Hall BA, Zakharenko SS, Winton DJ, Zhu L, Gilbertson RJ, Lourenço FC. The NALCN channel regulates metastasis and nonmalignant cell dissemination. Nat Genet. 2022 12; 54(12):1827-1838. PMID: 36175792; PMCID: PMC9729110.
      Citations: 16     Fields:    Translation:HumansAnimals
    13. Pedro L, Swietlik JJ, Shorthouse D, Haas L, Young T, da Costa ASH, Davidson S, Hall BA, Frezza C, Oskarsson T, Shields JD, Riedel A, Helal M, Schmitz W, Bhandare P, Wolf E. Tumor-Derived Lactic Acid Modulates Activation and Metabolic Status of Draining Lymph Node Stroma. Cancer Immunol Res. 2022 04 01; 10(4):482-497. PMID: 35362044; PMCID: PMC7612582.
      Citations: 6     Fields:    Translation:HumansCells
    14. Kostiou V, Hall MWJ, Jones PH, Hall BA. Simulations reveal that different responses to cell crowding determine the expansion of p53 and Notch mutant clones in squamous epithelia. J R Soc Interface. 2021 10; 18(183):20210607. PMID: 34637643; PMCID: PMC8510697.
      Citations: 2     Fields:    Translation:AnimalsCells
    15. Colom B, Herms A, Hall MWJ, Dentro SC, King C, Sood RK, Alcolea MP, Piedrafita G, Fernandez-Antoran D, Ong SH, Fowler JC, Mahbubani KT, Saeb-Parsy K, Gerstung M, Hall BA, Jones PH. Mutant clones in normal epithelium outcompete and eliminate emerging tumours. Nature. 2021 10; 598(7881):510-514. PMID: 34646013; PMCID: PMC7612642.
      Citations: 45     Fields:    Translation:AnimalsCells
    16. Shorthouse D, Hall BA. SARS-CoV-2 Variants Are Selecting for Spike Protein Mutations That Increase Protein Stability. J Chem Inf Model. 2021 09 27; 61(9):4152-4155. PMID: 34472347.
      Citations: 7     Fields:    Translation:HumansCells
    17. Lee M, Shorthouse D, Mahen R, Hall BA, Venkitaraman AR. Cancer-causing BRCA2 missense mutations disrupt an intracellular protein assembly mechanism to disable genome maintenance. Nucleic Acids Res. 2021 06 04; 49(10):5588-5604. PMID: 33978741; PMCID: PMC8191791.
      Citations: 10     Fields:    Translation:HumansCells
    18. Kostiou V, Zhang H, Hall MWJ, Jones PH, Hall BA. Methods for analysing lineage tracing datasets. R Soc Open Sci. 2021 May 05; 8(5):202231. PMID: 34035949; PMCID: PMC8097194.
      Citations: 1     
    19. Shorthouse D, Hall MWJ, Hall BA. Computational Saturation Screen Reveals the Landscape of Mutations in Human Fumarate Hydratase. J Chem Inf Model. 2021 04 26; 61(4):1970-1980. PMID: 33848143.
      Citations: 5     Fields:    Translation:Humans
    20. Fowler JC, King C, Bryant C, Hall MWJ, Sood R, Ong SH, Earp E, Fernandez-Antoran D, Koeppel J, Dentro SC, Shorthouse D, Durrani A, Fife K, Rytina E, Milne D, Roshan A, Mahububani K, Saeb-Parsy K, Hall BA, Gerstung M, Jones PH. Selection of Oncogenic Mutant Clones in Normal Human Skin Varies with Body Site. Cancer Discov. 2021 02; 11(2):340-361. PMID: 33087317; PMCID: PMC7116717.
      Citations: 40     Fields:    Translation:HumansCells
    21. Colom B, Alcolea MP, Piedrafita G, Hall MWJ, Wabik A, Dentro SC, Fowler JC, Herms A, King C, Ong SH, Sood RK, Gerstung M, Martincorena I, Hall BA, Jones PH. Spatial competition shapes the dynamic mutational landscape of normal esophageal epithelium. Nat Genet. 2020 06; 52(6):604-614. PMID: 32424351; PMCID: PMC7116672.
      Citations: 42     Fields:    Translation:Animals
    22. Piedrafita G, Kostiou V, Wabik A, Colom B, Fernandez-Antoran D, Herms A, Murai K, Hall BA, Jones PH. A single-progenitor model as the unifying paradigm of epidermal and esophageal epithelial maintenance in mice. Nat Commun. 2020 03 18; 11(1):1429. PMID: 32188860; PMCID: PMC7080751.
      Citations: 29     Fields:    Translation:AnimalsCells
    23. Hall BA, Fisher J. Constructing and Analyzing Computational Models of Cell Signaling with BioModelAnalyzer. Curr Protoc Bioinformatics. 2020 03; 69(1):e95. PMID: 32078258.
      Citations: 2     Fields:    Translation:AnimalsCells
    24. Nik-Zainal S, Hall BA. Cellular survival over genomic perfection. Science. 2019 11 15; 366(6467):802-803. PMID: 31727818; PMCID: PMC6872451.
      Citations: 7     Fields:    Translation:HumansCells
    25. Hall MWJ, Jones PH, Hall BA. Relating evolutionary selection and mutant clonal dynamics in normal epithelia. J R Soc Interface. 2019 07 26; 16(156):20190230. PMID: 31362624; PMCID: PMC6685019.
      Citations: 10     Fields:    Translation:HumansCells
    26. Murai K, Skrupskelyte G, Piedrafita G, Hall M, Kostiou V, Ong SH, Nagy T, Cagan A, Goulding D, Klein AM, Hall BA, Jones PH. Epidermal Tissue Adapts to Restrain Progenitors Carrying Clonal p53 Mutations. Cell Stem Cell. 2018 11 01; 23(5):687-699.e8. PMID: 30269904; PMCID: PMC6224607.
      Citations: 38     Fields:    Translation:AnimalsCells
    27. Shorthouse D, Riedel A, Kerr E, Pedro L, Samarajiwa S, Martins CP, Shields J, Hall BA, Bihary D. Exploring the role of stromal osmoregulation in cancer and disease using executable modelling. Nat Commun. 2018 08 01; 9(1):3011. PMID: 30069015; PMCID: PMC6070494.
      Citations: 10     Fields:    Translation:HumansAnimalsCells
    28. Paterson YZ, Shorthouse D, Pleijzier MW, Piterman N, Bendtsen C, Hall BA, Fisher J. A toolbox for discrete modelling of cell signalling dynamics. Integr Biol (Camb). 2018 06 18; 10(6):370-382. PMID: 29855020.
      Citations: 2     Fields:    Translation:HumansCells
    29. Coats BR, Schoenfelt KQ, Peris E, Cui C, Hoffman A, Zhou G, Fernandez S, Zhai L, Hall BA, Haka AS, Shah AM, Reardon CA, Brady MJ, Rhodes CJ, Maxfield FR, Becker L, Barbosa-Lorenzi VC. Metabolically Activated Adipose Tissue Macrophages Perform Detrimental and Beneficial Functions during Diet-Induced Obesity. Cell Rep. 2017 Sep 26; 20(13):3149-3161. PMID: 28954231; PMCID: PMC5646237.
      Citations: 128     Fields:    Translation:HumansAnimalsCells
    30. Turrell FK, Kerr EM, Gao M, Thorpe H, Doherty GJ, Cridge J, Shorthouse D, Speed A, Samarajiwa S, Hall BA, Griffiths M, Martins CP. Lung tumors with distinct p53 mutations respond similarly to p53 targeted therapy but exhibit genotype-specific statin sensitivity. Genes Dev. 2017 07 01; 31(13):1339-1353. PMID: 28790158; PMCID: PMC5580655.
      Citations: 39     Fields:    Translation:AnimalsCells
    31. Riedel A, Shorthouse D, Haas L, Hall BA, Shields J. Tumor-induced stromal reprogramming drives lymph node transformation. Nat Immunol. 2016 09; 17(9):1118-27. PMID: 27400148; PMCID: PMC4994871.
      Citations: 75     Fields:    Translation:AnimalsCells
    32. Rogala KB, Baratchian M, Zamfir V, Kunze MB, Dagless S, Pirker KF, Collins MK, Hall BA, Barrett TE, Kay CW, Bagnéris C. Probing the solution structure of I?B kinase (IKK) subunit ? and its interaction with Kaposi sarcoma-associated herpes virus Flice-interacting protein and IKK subunit ß by EPR spectroscopy. J Biol Chem. 2015 Sep 18; 290(38):23024. PMID: 26386046; PMCID: PMC4645591.
      Citations: 1     Fields:    
    33. Hall BA, Piterman N, Hajnal A, Fisher J. Emergent stem cell homeostasis in the C. elegans germline is revealed by hybrid modeling. Biophys J. 2015 Jul 21; 109(2):428-38. PMID: 26200879; PMCID: PMC4621618.
      Citations: 7     Fields:    Translation:AnimalsCells
    34. Rogala KB, Baratchian M, Zamfir V, Kunze MB, Dagless S, Pirker KF, Collins MK, Hall BA, Barrett TE, Kay CW, Bagnéris C. Probing the Solution Structure of I?B Kinase (IKK) Subunit ? and Its Interaction with Kaposi Sarcoma-associated Herpes Virus Flice-interacting Protein and IKK Subunit ß by EPR Spectroscopy. J Biol Chem. 2015 Jul 03; 290(27):16539-49. PMID: 25979343; PMCID: PMC4505408.
      Citations: 11     Fields:    Translation:HumansCells
    35. Chuang R, Hall BA, Benque D, Cook B, Ishtiaq S, Piterman N, Taylor A, Vardi M, Koschmieder S, Gottgens B, Fisher J. Drug target optimization in chronic myeloid leukemia using innovative computational platform. Sci Rep. 2015 Feb 03; 5:8190. PMID: 25644994; PMCID: PMC4650822.
      Citations: 3     Fields:    Translation:Humans
    36. Hall BA, Jackson E, Hajnal A, Fisher J. Logic programming to predict cell fate patterns and retrodict genotypes in organogenesis. J R Soc Interface. 2014 Sep 06; 11(98):20140245. PMID: 24966232; PMCID: PMC4233684.
      Citations: 1     Fields:    Translation:AnimalsCells
    37. Hall BA, Halim KB, Buyan A, Emmanouil B, Sansom MS. Sidekick for Membrane Simulations: Automated Ensemble Molecular Dynamics Simulations of Transmembrane Helices. J Chem Theory Comput. 2014 May 13; 10(5):2165-75. PMID: 26580541; PMCID: PMC4871227.
      Citations: 10     Fields:    
    38. Wright DW, Hall BA, Kenway OA, Jha S, Coveney PV. Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors. J Chem Theory Comput. 2014 Mar 11; 10(3):1228-1241. PMID: 24683369; PMCID: PMC3966525.
      Citations: 44     Fields:    
    39. Reddy T, Manrique S, Buyan A, Hall BA, Chetwynd A, Sansom MS. Primary and secondary dimer interfaces of the fibroblast growth factor receptor 3 transmembrane domain: characterization via multiscale molecular dynamics simulations. Biochemistry. 2014 Jan 21; 53(2):323-32. PMID: 24397339; PMCID: PMC4871223.
      Citations: 13     Fields:    Translation:HumansCells
    40. Brickley DR, Agyeman AS, Kopp RF, Hall BA, Harbeck MC, Belova L, Volden PA, Wu W, Roe MW, Conzen SD. Serum- and glucocorticoid-induced protein kinase 1 (SGK1) is regulated by store-operated Ca2+ entry and mediates cytoprotection against necrotic cell death. J Biol Chem. 2013 Nov 08; 288(45):32708-32719. PMID: 24043625; PMCID: PMC3820905.
      Citations: 10     Fields:    Translation:HumansCells
    41. Skor MN, Wonder EL, Kocherginsky M, Goyal A, Hall BA, Cai Y, Conzen SD. Glucocorticoid receptor antagonism as a novel therapy for triple-negative breast cancer. Clin Cancer Res. 2013 Nov 15; 19(22):6163-72. PMID: 24016618; PMCID: PMC3860283.
      Citations: 93     Fields:    Translation:HumansAnimalsCells
    42. Decaen PG, Hall BA, Naylor CE, Clapham DE, Kay CW, Wallace BA, Bagnéris C. Role of the C-terminal domain in the structure and function of tetrameric sodium channels. Nat Commun. 2013; 4:2465. PMID: 24051986; PMCID: PMC3791462.
      Citations: 48     Fields:    Translation:Cells
    43. Parton DL, Hall BA, Steinhauer S, Brasseur R, Lins L, Sansom MS, Crowet JM. Multi-scale simulation of the simian immunodeficiency virus fusion peptide. J Phys Chem B. 2012 Nov 26; 116(46):13713-21. PMID: 23094791.
      Citations: 5     Fields:    Translation:Cells
    44. Vostrikov VV, Hall BA, Sansom MS, Koeppe RE. Accommodation of a central arginine in a transmembrane peptide by changing the placement of anchor residues. J Phys Chem B. 2012 Nov 01; 116(43):12980-90. PMID: 23030363; PMCID: PMC3486957.
      Citations: 13     Fields:    Translation:Cells
    45. Hall BA, Armitage JP, Sansom MS. Mechanism of bacterial signal transduction revealed by molecular dynamics of Tsr dimers and trimers of dimers in lipid vesicles. PLoS Comput Biol. 2012; 8(9):e1002685. PMID: 23028283; PMCID: PMC3447960.
      Citations: 20     Fields:    Translation:Cells
    46. Doux JP, Hall BA, Killian JA. How lipid headgroups sense the membrane environment: an application of ¹4N NMR. Biophys J. 2012 Sep 19; 103(6):1245-53. PMID: 22995497; PMCID: PMC3446661.
      Citations: 6     Fields:    Translation:Cells
    47. Lindau M, Hall BA, Chetwynd A, Beckstein O, Sansom MS. Coarse-grain simulations reveal movement of the synaptobrevin C-terminus in response to piconewton forces. Biophys J. 2012 Sep 05; 103(5):959-69. PMID: 23009845; PMCID: PMC3433613.
      Citations: 30     Fields:    Translation:AnimalsCells
    48. Hall BA, Wright DW, Jha S, Coveney PV. Quantized water access to the HIV-1 protease active site as a proposed mechanism for cooperative mutations in drug affinity. Biochemistry. 2012 Aug 21; 51(33):6487-9. PMID: 22866962.
      Citations: 3     Fields:    Translation:Cells
    49. Hall BA, Kim TY, Skor MN, Conzen SD. Serum and glucocorticoid-regulated kinase 1 (SGK1) activation in breast cancer: requirement for mTORC1 activity associates with ER-alpha expression. Breast Cancer Res Treat. 2012 Sep; 135(2):469-79. PMID: 22842983; PMCID: PMC3891577.
      Citations: 21     Fields:    Translation:HumansCells
    50. Wright DW, Hall BA, Kellam P, Coveney PV. Global Conformational Dynamics of HIV-1 Reverse Transcriptase Bound to Non-Nucleoside Inhibitors. Biology (Basel). 2012 Jul 26; 1(2):222-44. PMID: 24832224; PMCID: PMC4009785.
      Citations: 5     
    51. Gregg BE, Moore PC, Demozay D, Hall BA, Li M, Husain A, Wright AJ, Atkinson MA, Rhodes CJ. Formation of a human ß-cell population within pancreatic islets is set early in life. J Clin Endocrinol Metab. 2012 Sep; 97(9):3197-206. PMID: 22745242; PMCID: PMC3431572.
      Citations: 187     Fields:    Translation:HumansCells
    52. Hall BA, Armitage JP, Sansom MS. Transmembrane helix dynamics of bacterial chemoreceptors supports a piston model of signalling. PLoS Comput Biol. 2011 Oct; 7(10):e1002204. PMID: 22028633; PMCID: PMC3197627.
      Citations: 27     Fields:    Translation:Cells
    53. Kalli AC, Hall BA, Campbell ID, Sansom MS. A helix heterodimer in a lipid bilayer: prediction of the structure of an integrin transmembrane domain via multiscale simulations. Structure. 2011 Oct 12; 19(10):1477-84. PMID: 22000516; PMCID: PMC3195670.
      Citations: 15     Fields:    Translation:AnimalsCells
    54. Watson AA, Lebedev AA, Hall BA, Fenton-May AE, Vagin AA, Dejnirattisai W, Felce J, Mongkolsapaya J, Palma AS, Liu Y, Feizi T, Screaton GR, Murshudov GN, O'Callaghan CA. Structural flexibility of the macrophage dengue virus receptor CLEC5A: implications for ligand binding and signaling. J Biol Chem. 2011 Jul 08; 286(27):24208-18. PMID: 21566123; PMCID: PMC3129202.
      Citations: 23     Fields:    Translation:HumansCells
    55. Hall BA, Chetwynd AP, Sansom MS. Exploring peptide-membrane interactions with coarse-grained MD simulations. Biophys J. 2011 Apr 20; 100(8):1940-8. PMID: 21504730; PMCID: PMC3077683.
      Citations: 16     Fields:    Translation:Cells
    56. Vohra S, Hall BA, Holdbrook DA, Khalid S, Biggin PC. Bookshelf: a simple curation system for the storage of biomolecular simulation data. Database (Oxford). 2010; 2010:baq033. PMID: 21169341; PMCID: PMC3004466.
      Citations: 5     Fields:    Translation:Cells
    57. Chetwynd A, Wee CL, Hall BA, Sansom MS. The energetics of transmembrane helix insertion into a lipid bilayer. Biophys J. 2010 Oct 20; 99(8):2534-40. PMID: 20959094; PMCID: PMC2955506.
      Citations: 13     Fields:    Translation:Cells
    58. Vostrikov VV, Hall BA, Greathouse DV, Koeppe RE, Sansom MS. Changes in transmembrane helix alignment by arginine residues revealed by solid-state NMR experiments and coarse-grained MD simulations. J Am Chem Soc. 2010 Apr 28; 132(16):5803-11. PMID: 20373735; PMCID: PMC2888137.
      Citations: 47     Fields:    Translation:Cells
    59. Hall BA, Sansom MS. Coarse-Grained MD Simulations and Protein-Protein Interactions: The Cohesin-Dockerin System. J Chem Theory Comput. 2009 Sep 08; 5(9):2465-71. PMID: 26616626.
      Citations: 9     Fields:    
    60. Hall BA, Kaye SL, Pang A, Perera R, Biggin PC. Characterization of protein conformational states by normal-mode frequencies. J Am Chem Soc. 2007 Sep 19; 129(37):11394-401. PMID: 17715919.
      Citations: 7     Fields:    Translation:Cells
    61. Haider S, Hall BA, Sansom MS. Simulations of a protein translocation pore: SecY. Biochemistry. 2006 Oct 31; 45(43):13018-24. PMID: 17059218.
      Citations: 14     Fields:    Translation:Cells
    62. Haider S, Grottesi A, Hall BA, Ashcroft FM, Sansom MS. Conformational dynamics of the ligand-binding domain of inward rectifier K channels as revealed by molecular dynamics simulations: toward an understanding of Kir channel gating. Biophys J. 2005 May; 88(5):3310-20. PMID: 15749783; PMCID: PMC1305479.
      Citations: 14     Fields:    Translation:AnimalsCells
    63. Barrett CP, Hall BA, Noble ME. Dynamite: a simple way to gain insight into protein motions. Acta Crystallogr D Biol Crystallogr. 2004 Dec; 60(Pt 12 Pt 1):2280-7. PMID: 15572782.
      Citations: 40     Fields:    Translation:Cells
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