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    Barry Grant

    TitleLecturer
    SchoolUniversity of California, San Diego
    DepartmentMolecular Biology
    Address9500 Gilman Drive #0355
    CA La Jolla 92093
    Phone858-822-2209
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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Yao XQ, Cato MC, Labudde E, Beyett TS, Tesmer JJG, Grant B. Navigating the conformational landscape of G protein-coupled receptor kinases during allosteric activation. J Biol Chem. 2017 Aug 14. PMID: 28808053.
        View in: PubMed
      2. Jariwala S, Skjærven L, Yao XQ, Grant B. Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web. J Vis Exp. 2017 Jul 16; (125). PMID: 28745621.
        View in: PubMed
      3. Prakash P, Sayyed-Ahmad A, Cho KJ, Dolino DM, Chen W, Li H, Grant B, Hancock JF, Gorfe AA. Computational and biochemical characterization of two partially overlapping interfaces and multiple weak-affinity K-Ras dimers. Sci Rep. 2017 Jan 09; 7:40109. PMID: 28067274.
        View in: PubMed
      4. Nwachukwu JC, Srinivasan S, Bruno NE, Nowak J, Wright NJ, Minutolo F, Rangarajan ES, Izard T, Yao XQ, Grant B, Kojetin DJ, Elemento O, Katzenellenbogen JA, Nettles KW. Systems Structural Biology Analysis of Ligand Effects on ERa Predicts Cellular Response to Environmental Estrogens and Anti-hormone Therapies. Cell Chem Biol. 2017 Jan 19; 24(1):35-45. PMID: 28042045.
        View in: PubMed
      5. Skjærven L, Jariwala S, Yao XQ, Grant B. Online interactive analysis of protein structure ensembles with Bio3D-web. Bioinformatics. 2016 Nov 15; 32(22):3510-3512. PMID: 27423893.
        View in: PubMed
      6. Yao XQ, Skjærven L, Grant B. Rapid Characterization of Allosteric Networks with Ensemble Normal Mode Analysis. J Phys Chem B. 2016 Aug 25; 120(33):8276-88. PMID: 27056373.
        View in: PubMed
      7. Yao XQ, Malik RU, Griggs NW, Skjærven L, Traynor JR, Sivaramakrishnan S, Grant B. Dynamic Coupling and Allosteric Networks in the a Subunit of Heterotrimeric G Proteins. J Biol Chem. 2016 Feb 26; 291(9):4742-53. PMID: 26703464; PMCID: PMC4813496 [Available on 02/26/17].
      8. Scarabelli G, Soppina V, Yao XQ, Atherton J, Moores CA, Verhey KJ, Grant B. Mapping the Processivity Determinants of the Kinesin-3 Motor Domain. Biophys J. 2015 Oct 20; 109(8):1537-40. PMID: 26488644; PMCID: PMC4624112.
      9. Kalenkiewicz A, Grant B, Yang CY. Enrichment of druggable conformations from apo protein structures using cosolvent-accelerated molecular dynamics. Biology (Basel). 2015 Apr 21; 4(2):344-66. PMID: 25906084; PMCID: PMC4498304.
      10. Skjærven L, Yao XQ, Scarabelli G, Grant B. Integrating protein structural dynamics and evolutionary analysis with Bio3D. BMC Bioinformatics. 2014 Dec 10; 15:399. PMID: 25491031; PMCID: PMC4279791.
      11. Scarabelli G, Grant B. Kinesin-5 allosteric inhibitors uncouple the dynamics of nucleotide, microtubule, and neck-linker binding sites. Biophys J. 2014 Nov 04; 107(9):2204-13. PMID: 25418105; PMCID: PMC4223232.
      12. Scarabelli G, Grant B. Mapping the structural and dynamical features of kinesin motor domains. PLoS Comput Biol. 2013; 9(11):e1003329. PMID: 24244137; PMCID: PMC3820509.
      13. Yao XQ, Grant B. Domain-opening and dynamic coupling in the a-subunit of heterotrimeric G proteins. Biophys J. 2013 Jul 16; 105(2):L08-10. PMID: 23870276; PMCID: PMC3714883.
      14. Kekenes-Huskey PM, Metzger VT, Grant B, Andrew McCammon J. Calcium binding and allosteric signaling mechanisms for the sarcoplasmic reticulum Ca²+ ATPase. Protein Sci. 2012 Oct; 21(10):1429-43. PMID: 22821874; PMCID: PMC3526986.
      15. Ortiz-Sanchez JM, Nichols SE, Sayyah J, Brown JH, McCammon JA, Grant B. Identification of potential small molecule binding pockets on Rho family GTPases. PLoS One. 2012; 7(7):e40809. PMID: 22815826; PMCID: PMC3397943.
      16. Thomas JR, Gedeon PC, Grant B, Madura JD. LeuT conformational sampling utilizing accelerated molecular dynamics and principal component analysis. Biophys J. 2012 Jul 03; 103(1):L1-3. PMID: 22828348; PMCID: PMC3388204.
      17. Ostrov DA, Grant B, Pompeu YA, Sidney J, Harndahl M, Southwood S, Oseroff C, Lu S, Jakoncic J, de Oliveira CA, Yang L, Mei H, Shi L, Shabanowitz J, English AM, Wriston A, Lucas A, Phillips E, Mallal S, Grey HM, Sette A, Hunt DF, Buus S, Peters B. Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire. Proc Natl Acad Sci U S A. 2012 Jun 19; 109(25):9959-64. PMID: 22645359; PMCID: PMC3382472.
      18. Grant B, Gheorghe DM, Zheng W, Alonso M, Huber G, Dlugosz M, McCammon JA, Cross RA. Electrostatically biased binding of kinesin to microtubules. PLoS Biol. 2011 Nov; 9(11):e1001207. PMID: 22140358; PMCID: PMC3226556.
      19. Bucher D, Grant B, McCammon JA. Induced fit or conformational selection? The role of the semi-closed state in the maltose binding protein. Biochemistry. 2011 Dec 06; 50(48):10530-9. PMID: 22050600; PMCID: PMC3226325.
      20. Grant B, Lukman S, Hocker HJ, Sayyah J, Brown JH, McCammon JA, Gorfe AA. Novel allosteric sites on Ras for lead generation. PLoS One. 2011; 6(10):e25711. PMID: 22046245; PMCID: PMC3201956.
      21. de Oliveira CA, Grant B, Zhou M, McCammon JA. Large-scale conformational changes of Trypanosoma cruzi proline racemase predicted by accelerated molecular dynamics simulation. PLoS Comput Biol. 2011 Oct; 7(10):e1002178. PMID: 22022240; PMCID: PMC3192803.
      22. Bucher D, Grant B, Markwick PR, McCammon JA. Accessing a hidden conformation of the maltose binding protein using accelerated molecular dynamics. PLoS Comput Biol. 2011 Apr; 7(4):e1002034. PMID: 21533070; PMCID: PMC3080849.
      23. Skjaerven L, Grant B, Muga A, Teigen K, McCammon JA, Reuter N, Martinez A. Conformational sampling and nucleotide-dependent transitions of the GroEL subunit probed by unbiased molecular dynamics simulations. PLoS Comput Biol. 2011 Mar; 7(3):e1002004. PMID: 21423709; PMCID: PMC3053311.
      24. Grant B, McCammon JA, Gorfe AA. Conformational selection in G-proteins: lessons from Ras and Rho. Biophys J. 2010 Dec 01; 99(11):L87-9. PMID: 21112273; PMCID: PMC2998626.
      25. Lukman S, Grant B, Gorfe AA, Grant GH, McCammon JA. The distinct conformational dynamics of K-Ras and H-Ras A59G. PLoS Comput Biol. 2010 Sep 09; 6(9). PMID: 20838576; PMCID: PMC2936511.
      26. Grant B, Gorfe AA, McCammon JA. Large conformational changes in proteins: signaling and other functions. Curr Opin Struct Biol. 2010 Apr; 20(2):142-7. PMID: 20060708; PMCID: PMC2866511.
      27. Khavrutskii IV, Grant B, Taylor SS, McCammon JA. A transition path ensemble study reveals a linchpin role for Mg(2+) during rate-limiting ADP release from protein kinase A. Biochemistry. 2009 Dec 08; 48(48):11532-45. PMID: 19886670; PMCID: PMC2789581.
      28. Gallo MT, Grant B, Teodoro ML, Melton J, Cieplak P, Phillips GN, Stec B. Novel procedure for thermal equilibration in molecular dynamics simulation. Mol Simul. 2009 Apr 01; 35(5):349-357. PMID: 25125797.
        View in: PubMed
      29. Grant B, Gorfe AA, McCammon JA. Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics. PLoS Comput Biol. 2009 Mar; 5(3):e1000325. PMID: 19300489; PMCID: PMC2651530.
      30. Gorfe AA, Grant B, McCammon JA. Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins. Structure. 2008 Jun; 16(6):885-96. PMID: 18547521; PMCID: PMC2519881.
      31. Rodrigues AP, Grant B, Godzik A, Friedberg I. The 2006 automated function prediction meeting. BMC Bioinformatics. 2007 May 22; 8 Suppl 4:S1-4. PMID: 17570143; PMCID: PMC1892079.
      32. Grant B, McCammon JA, Caves LS, Cross RA. Multivariate analysis of conserved sequence-structure relationships in kinesins: coupling of the active site and a tubulin-binding sub-domain. J Mol Biol. 2007 May 18; 368(5):1231-48. PMID: 17399740.
        View in: PubMed
      33. Grant B, Rodrigues AP, ElSawy KM, McCammon JA, Caves LS. Bio3d: an R package for the comparative analysis of protein structures. Bioinformatics. 2006 Nov 01; 22(21):2695-6. PMID: 16940322.
        View in: PubMed
      34. Cheng X, Wang H, Grant B, Sine SM, McCammon JA. Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors. PLoS Comput Biol. 2006 Sep 29; 2(9):e134. PMID: 17009865; PMCID: PMC1584325.
      35. Rodrigues AP, Grant B, Hubbard RE. sgTarget: a target selection resource for structural genomics. Nucleic Acids Res. 2006 Jul 01; 34(Web Server issue):W225-30. PMID: 16844998; PMCID: PMC1538879.
      36. Cheng X, Lu B, Grant B, Law RJ, McCammon JA. Channel opening motion of alpha7 nicotinic acetylcholine receptor as suggested by normal mode analysis. J Mol Biol. 2006 Jan 13; 355(2):310-24. PMID: 16307758.
        View in: PubMed
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