Publications

Lu M, Dousis AD, Ma J. OPUS-Rota: a fast and accurate method for side-chain modeling. Protein Sci. 2008 Sep;17(9):1576-85. Pubmed PMID: 18556476

Lu M, Ma J. A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography. Proc Natl Acad Sci U S A. 2008 Oct 7;105(40):15358-63. Pubmed PMID: 18832168

Ma J. Explicit orientation dependence in empirical potentials and its significance to side-chain modeling. Acc Chem Res. 2009 Aug 18;42(8):1087-96. Pubmed PMID: 19445451

Chen X, Lu M, Poon BK, Wang Q, Ma J. Structural improvement of unliganded simian immunodeficiency virus gp120 core by normal-mode-based X-ray crystallographic refinement. Acta Crystallogr D Biol Crystallogr. 2009 Apr;65(Pt 4):339-47. Pubmed PMID: 19307715

Chen X, Wang Q, Ni F, Ma J. Structure of the full-length Shaker potassium channel Kv1.2 by normal-mode-based X-ray crystallographic refinement. Proc Natl Acad Sci U S A. 2010 Jun 22;107(25):11352-7. Pubmed PMID: 20534430

Lu M, Ma J. Normal mode analysis with molecular geometry restraints: bridging molecular mechanics and elastic models. Arch Biochem Biophys. 2011 Apr 1;508(1):64-71. Pubmed PMID: 21211510

Murphy DR, Reis B, Kadiyala H, Hirani K, Sittig DF, Khan MM, Singh H. Electronic health record-based messages to primary care providers: valuable information or just noise? Arch Intern Med. 2012 Feb 13;172(3):283-5. Pubmed PMID: 22332167

Zeng J, Kirk BD, Gou Y, Wang Q, Ma J. Genome-wide polycomb target gene prediction in Drosophila melanogaster. Nucleic Acids Res. 2012 Jul;40(13):5848-63. Pubmed PMID: 22416065

Lu M, Ming D, Ma J. fSUB: normal mode analysis with flexible substructures. J Phys Chem B. 2012 Jul 26;116(29):8636-45. Pubmed PMID: 22448847

Lu M, Ma J. PIM: phase integrated method for normal mode analysis of biomolecules in a crystalline environment. J Mol Biol. 2013 Mar 25;425(6):1082-98. Pubmed PMID: 23333742