BinXue

Bin Xue, PhD

Assistant Professor, Non Usf Health

College Of Medicine Molecular Medicine

Contact Info 12901 Bruce B Downs Blvd
MDC 7
Tampa, FL 33612

Academic Email: bxue@health.usf.edu

Academic Phone: (813) 974-1905

Education

  • PhD, Physics, Nanjing University, 2005
  • PhD, Condensed Matter Physics, Nanjing University, 2005

Research Interests

  • I am fascinated by questions related to protein sequence-conformation-function and roles of protein molecules and their interactions in the process of development, evolution, and human diseases.
  • In all these questions, protein conformation and conformational changes play key roles. Many proteins have specific 3-dimensional structures to perform their functions. Meanwhile, more proteins have been found without rigid 3-dimensional structures under physiological conditions. These two types of proteins are usually called structured proteins and intrinsically disordered proteins.
  • I am using various computational tools to study these two types of proteins. Current projects include:
  • - Machine-learning based prediction of protein intrinsic disorder and structural properties;
  • - Molecular simulation of proteins;
  • - Docking;
  • - Protein interaction pathways and networks;
  • - Molecular mechanisms of diseases;
  • - Theoretical topics on computational molecular biology and biophysics;
  • - etc.

Recent Publications

  • Xue, B.Soeria-Atmadja, D.Gustafsson, MG.Hammerling, U.Dunker, AK.Uversky, VN. Abundance and functional roles of intrinsic disorder in allergenic proteins and allergen representative peptides. Proteins. , 2011. http://www.ncbi.nlm.nih.gov/pubmed/21732419
  • Xue, B.Oldfield, CJ.Van, YY.Dunker, AK.Uversky, VN. Protein intrinsic disorder and induced pluripotent stem cells. Molecular bioSystems. , 2011. http://www.ncbi.nlm.nih.gov/pubmed/21761058
  • Xue, B.Williams, RW.Oldfield, CJ.Dunker, AK.Uversky, VN. Archaic chaos: intrinsically disordered proteins in Archaea. BMC systems biology. 4 Suppl 1: S1, 2010. http://www.ncbi.nlm.nih.gov/pubmed/20522251
  • Xue, B.Dunker, AK.Uversky, VN. Retro-MoRFs: Identifying Protein Binding Sites by Normal and Reverse Alignment and Intrinsic Disorder Prediction. International journal of molecular sciences. 11(10) : 3725-47, 2010. http://www.ncbi.nlm.nih.gov/pubmed/21152297
  • Xue, B.Hsu, WL.Lee, JH.Lu, H.Dunker, AK.Uversky, VN. SPA: Short peptide analyzer of intrinsic disorder status of short peptides. Genes to cells : devoted to molecular & cellular mechanisms. 15(6) : 635-46, 2010. http://www.ncbi.nlm.nih.gov/pubmed/20497238
  • Xue, B.Dunbrack, RL.Williams, RW.Dunker, AK.Uversky, VN. PONDR-FIT: a meta-predictor of intrinsically disordered amino acids. Biochimica et biophysica acta. 1804(4) : 996-1010, 2010. http://www.ncbi.nlm.nih.gov/pubmed/20100603
  • Xue, B.Williams, RW.Oldfield, CJ.Goh, GK.Dunker, AK.Uversky, VN. Viral disorder or disordered viruses: do viral proteins possess unique features? Protein and peptide letters. 17(8) : 932-51, 2010. http://www.ncbi.nlm.nih.gov/pubmed/20450483
  • Xue, B.Li, L.Meroueh, SO.Uversky, VN.Dunker, AK. Analysis of structured and intrinsically disordered regions of transmembrane proteins. Molecular bioSystems. 5(12) : 1688-1702, 2009. http://www.ncbi.nlm.nih.gov/pubmed/19585006
  • Xue, B.Dor, O.Faraggi, E.Zhou, Y. Real-value prediction of backbone torsion angles. Proteins. 72(1) : 427-33, 2008. http://www.ncbi.nlm.nih.gov/pubmed/18214956
  • Xue, B; Su, Y; Wang, W. Permeation of particle through a four-helix-bundle model channel J. Chem. Phys.. 122(10) : 104703, 2005.