Recent Publications

• Online interactive analysis of protein structure ensembles with Bio3D-web.
  Skjærven, Jariwala, Yao, Grant. (2016)
  Bioinformatics (2016) [In Press. Epub ahead of print]
  ( Journal | PubMed | PDF | WebServer )

• Rapid characterization of allosteric networks with ensemble normal mode analysis.
  Yao, Skjærven, Grant. (2016)
  J Phys Chem B. 2016 Apr 20. [Epub ahead of print]
  ( Journal | PubMed | PDF )

• Dynamic coupling and allosteric networks in the alpha subunit of heterotrimeric G proteins.
  Yao, Malik, Griggs, Skjaerven, Traynor, Sivaramakrishnan, Grant (2016)
  J Biol Chem. 291(9), 4742-4753.
  ( Journal | PubMed | PDF )

• Mapping the processivity determinants of the kinesin-3 motor domain.
  Scarabelli, Soppina, Yao, Atherton, Moores, Verhey, Grant (2015)
  Biophys J. 109, 1537–1540.
  ( Journal | PubMed | PDF )

• Enrichment of druggable conformations from apo protein structures using cosolvent-accelerated molecular dynamics.
  Kalenkiewicz, Grant, Yang (2015)
  Biology. 4, 344-366
  ( Journal | PubMed | PDF )

• Integrating protein structural dynamics and evolutionary analysis with Bio3D.
  Skjærven, Yao, Scarabelli, Grant (2014)
  BMC Bioinformatics. 15, 399
  ( Journal | PubMed | PDF )

• Kinesin-5 allosteric inhibitors uncouple the dynamics of nucleotide, microtubule and neck-linker binding sites.
  Scarabelli, Grant (2014)
  Biophys J. 107, 2204–2213
  ( Journal | PubMed | PDF )

• Mapping the structural and dynamical features of kinesin motor domains.
  Scarabelli, Grant (2013)
  PLoS Comput Biol. 9, e1003329
  ( Journal | PubMed | PDF )

• Domain opening and dynamic coupling in the alpha subunit of heterotrimeric G proteins.
  Yao, Grant (2013)
  Biophys J. 105, L08–L10
  ( Journal | PubMed | PDF )

• Identification of potential small molecule binding pockets on Rho family GTPases.
  Ortiz Sanchez, Nichols, Sayyah, Heller Brown, McCammon, Grant (2012)
  PLoS One. 7, e40809
  ( Journal | PubMed | PDF )

• Calcium binding and allosteric signaling mechanisms for Sarcoplasmic reticulum Ca2+ ATPase.
  Kekenes-Huskey, Metzger, Grant, McCammon (2012)
  Protein Science. 10, 1429-43
  ( Journal | PubMed | PDF )

• Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire.
  Ostrov, Grant, Pompeu, Sidney, Harndahl, Southwood, Oseroff, Lu, Jakoncic, de Oliveira, Yang, Mei, Shi, Shabanowitz, English, Wriston, Lucas, Phillips, Mallal, Grey, Sette, Hunt, Buus, Peters (2012)
  PNAS. 109, 9959-64.
  ( Journal | PubMed | PDF )

• LeuT conformational sampling utilizing accelerated molecular dynamics and principal component analysis.
  Thomas, Gedeon, Grant, Madura (2012)
  Biophys J. 103, L1-3
  ( Journal | PubMed | PDF )

Pre Michigan Publications

The following publications where from UCSD

• Electrostatically biased binding of kinesin to microtubules.
  Grant, Gheorghe, Zheng, Alonso, Huber, Dlugosz, McCammon, Cross (2011)
  PLoS Biology. 9, e1001207
  ( Journal | PubMed | PDF | Press: 1, 2, 3)

• Induced-fit or conformational selection? The role of the semi-closed state in the Maltose Binding Protein.
  Bucher, Grant, McCammon (2011)
  Biochemistry. 50, 10530–10539
  ( Journal | PubMed | PDF )

• Novel allosteric sites on Ras for lead generation.
  Grant, Lukman, Hocker, Sayyah, Heller Brown, McCammon, Gorfe (2011)
  PLoS One. 6, e25711
  ( Journal | PubMed | PDF )

• Large-scale conformational changes of Trypanosoma cruzi proline racemase predicted by accelerated molecular dynamics simulation.
  Oliveira*, Grant*, Zhou, McCammon (2011)
  PLoS Comput Biol. 7, e1002178
  ( Journal | PubMed | PDF )

• Accessing a hidden conformation of the maltose binding protein with accelerated molecular dynamics.
  Bucher, Grant, Markwick, McCammon (2011)
  PLoS Comput Biol. 7, e1002004
  ( Journal | PubMed | PDF )

• Conformational sampling and nucleotide-dependent transitions of the GroEL subunit probed by unbiased molecular dynamics simulations.
  Skjaerven, Grant, Muga, Teigen, McCammon, Reuter and Martinez (2011)
  PLoS Comput Biol. 7, e1002004
  ( Journal | PubMed | PDF )

• Conformational selection in G-proteins: lessons from Ras and Rho.
  Grant, Mccammon, Gorfe (2010)
  Biophys J. 99, L87-L89
  ( Journal | PubMed | PDF )

• The distinct conformational dynamics of K-Ras and H-Ras A59G.
  Lukman*, Grant*, Gorfe, Mccammon (2010)
  PLoS Comput Biol. 6, e1000922
  ( Journal | PubMed | PDF )

• Large conformational changes in proteins: signaling and other functions.
  Grant, Gorfe, Mccammon (2010)
  Current Opinion in Structural Biology. 20, 142-147
  ( Journal | PubMed | PDF )

• A transition path ensemble study reveals a linchpin role for Mg2+ during rate-limiting ADP release from protein kinase A.
  Khavrutskii, Grant, Taylor, Mccammon (2009)
  Biochemistry. 48, 11532-11545
  ( Journal | PubMed | PDF )

• Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics.
  Grant*, Gorfe*, Mccammon (2009)
  PLoS Comput Biol. 5, e1000325
  ( Journal | PubMed | PDF )

• Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins.
  Gorfe*, Grant*, Mccammon (2008)
  Structure. 16, 885-896
  ( Journal | PubMed | PDF )

• Novel procedure for thermal equilibration in molcecular dynamics simulations.
  Gallo, Grant, Teodoro, Melton, Cieplak, Phillips, Stec (2008)
  Molecular Simulation. 35, 349-357
  ( Journal | PubMed | PDF )

• Automated function prediction.
  Friedberg, Rodrigues, Grant, Godzik (2007)
  BMC Bioinformatics. 8, Suppl 4
  ( Abstract | PubMed | PDF )

• Multivariate analysis of conserved sequence-structure relationships in kinesins: coupling of the active site and a tubulin-binding sub-domain.
  Grant, McCammon, Caves, Cross (2007)
  Journal of Molecular Biology. 368, 1231-1248
  ( Journal | PubMed | PDF | F1000 )

• Bio3D: An R package for the comparative analysis of protein structures.
  Grant, Rodrigues, ElSawy, McCammon, Caves, (2006)
  Bioinformatics. 22, 2695-2696
  ( Journal | PubMed | PDF )

• Targeted molecular dynamics study of C-Loop closure and channel gating in nicotinic receptors.
  Cheng, Wang, Grant, Sine, McCammon (2006)
  PLoS Comput Biol. 2, No. 9.
  ( Journal | PubMed | PDF )

• sgTarget: a target selection resource for structural genomics.
  Rodrigues, Grant, Hubbard (2006)
  Nucleic Acids Res. 34, No. Web Server issue.
  ( Journal | PubMed | PDF )

• Channel opening motion of [alpha]7 nicotinic acetylcholine receptor as suggested by normal mode analysis.
  Cheng, Lu, Grant, Law, Mccammon (2006)
  Journal of Molecular Biology. 355, No. 2. 310-324.
  ( Journal | PubMed | PDF )