Yang Shen

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  • iCFN: interconnected cost function networks for multi-state protein design

Selected Papers (All)

(* Corresponding Author; ^ Equal Contributions)

Selected Presentations

  • “On Conformational Changes Associated with Protein-Protein Interactions: Normal Mode Analysis for Encounter Complexes” (with T Oliwa), invited talk, 2014 Protein Folding Conference, July 16–19, 2014, Punta Cana, Dominican Republic.
  • “A Complex-Based Normal Mode Analysis for Conformational Changes upon Protein Binding” (with T Oliwa), poster, 10th 3DSIG: ISMB Satellite Meeting on Structural Bioinformatics and Computational Biophysics (3DSIG’14), July 11-12, 2014, Boston, Massachusetts.
  • “New results on predicting and disrupting protein–protein interactions”, selected as oral presentation from exemplary submitted abstracts, Protein Discovery 2013 Summit -- Protein–Protein Interaction, Oct. 23–25, 2013, San Diego, California.
  • “Deciphering and overcoming mutation-based resistance to antiandrogens” (with GL Greene and CL Sawyers et al.), poster, 9th 3DSIG: ISMB Satellite Meeting on Structural Bioinformatics and Computational Biophysics (3DSIG’13), July 19-20, 2013, Berlin, Germany.
  • “Improved flexible refinement of protein docking in CAPRI rounds 22-27”, invited talk, 5th CAPRI (Critical Assessment of PRedicted Interactions) Evaluation Meeting (CAPRI'13), Apr. 17-19, 2013, Utrecht, The Netherlands.
  • “Designing and unraveling promiscuous inhibitors against drug-resistant target mutations” (with ML Radharishnan and B Tidor), invited talk, 245th American Chemical Society National Meeting (ACS'13-S), Apr. 7-11, 2013, New Orleans, Louisiana.
  • “Exploring molecular mechanisms for androgen receptor antagonism and agonism-conferring mutation” (with MD Balbas, MJ Evans, DJ Hosfield, GL Greene, and CL Sawyers), poster, 6th Conference on Modeling of Protein Interactions (MPI’12), Nov. 8-10, 2012, Lawrence, Kansas.
  • “Targeting drug-resistant HIV-1 protease mutants using inherent protein flexibility” (with B Tidor), poster, 8th 3DSIG: ISMB Satellite Meeting on Structural Bioinformatics and Computational Biophysics (3DSIG’12), July 13-14, 2012, Long Beach, California.
  • “Designing promiscuous inhibitors: Lessons learned from HIV-1 protease inhibition” (with M Radhakrishnan and B Tidor), oral presentation, 241st American Chemical Society National Meeting (ACS’11-S), Mar. 27–31, 2011, Anaheim, California.
A poster was presented at the 25th Annual Meeting of the Groups Studying the Structures of AIDS-Related Systems and Their Application to Targeted Drug Design, Mar. 28–30, 2011, National Institutes of Health, Bethesda, Maryland.
  • “Charge optimization of flexible ligands” (with MK Gilson and B Tidor), poster, 23rd Annual Symposium of the Protein Society (PS’09), Jul. 24–29, 2009, Boston, Massachusetts.
  • “Docking refinement by the underestimation of free energy funnels”, invited talk, 4th Conference on Modeling of Protein Interactions (MPI’07), Sept. 30–Oct. 2, 2007, Lawrence, Kansas.
  • “Structural similarity of binding sites in analogous enzymes” (with D Beglov, R Brenke, D Kozakov, and S Vajda), oral presentation, 234th ACS National Meeting (ACS’07-F), Aug. 19–23, 2007, Boston, Massachusetts.

Contributed Conference Abstracts

Presenters' names are highlighted in bold fonts.
  • “Integrated understanding of the metabolic and gene regulatory systems of Shewanella oneidensis MR-1” (with QK Beg, DK Byrne , ME Driscoll, FS Juhn, JJ Faith, ICh Paschalidis, TS Gardner and D Segrè), poster, 108th Annual Meeting of the American Society of Microbiology (ASM’08), Jun. 1–5, 2008, Boston, Massachusetts.
  • “Systematic identification of regulatory mapping and optimal metabolic engineering strategies in Shewanella oneidensis MR-1” (with DK Byrne, QK Beg, ME Driscoll, FS Juhn, JJ Faith, ICh Paschalidis, D Segrè, and TS Gardner), poster, U.S. Department of Energy Joint Genomics: GTL Awardee Workshop VI and Metabolic Engineering 2008 (GTL’08), Feb. 10–13, 2008, Bethesda, Maryland.
  • “Identification of druggable binding sites of proteins by computational fragment mapping using novel FFT correlation based algorithm” (with R Brenke, D Kozakov, D Beglov, G-Y Chuang, MR Landon, and S Vajda), oral presentation,15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB’07), Jul. 21–25, 2007, Vienna, Austria.
  • “Density-based characterization of hot spots by computational solvent mapping of proteins and applications to accurate three-dimensional pharmacophore generation” (with MR Landon, D Kozakov, R Brenke, T Baumeister, F Guarnieri, and S Vajda), poster, 15th Annual International Conference on ISMB (ISMB’07), Jul. 21–25, 2007, Vienna, Austria.
  • “Identification and characterization of hot spot regions in druggable protein binding sites by computational solvent mapping” (with MR Landon, S Vajda, D Kozakov, R Brenke, D Lancia, T Baumeister, and S Thiel), 233rd ACS National Meeting
    (ACS’07-S), Mar. 25–29, 2007, Chicago, Illinois.