Yang Shen

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We are proud to provide the non-commercial and not-for-profit use of our algorithms for free. Check out our codes at https://github.com/Shen-Lab

  • cNMA: contact-specific NMA for protein conformational change Codes Web Server Video
  • Notes on how to use the web server virtual machine: After installing VirtualBox, click File->Import Appliance and choose the .ova file. VirtualBox will import this machine. Choose the machine and click Start. After logging in with the password cNMA, click the firefox icon on the left panel and the web server will be loaded on the home page.

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

Selected Papers (Click here for all papers)

(* Corresponding Author; ^ Equal Contributions)

  • Y Cao, T Chen, Z Wang and Y Shen* (2019) Learning to Optimize in Swarms. Advances in Neural Information Processing Systems (NeurIPS 2019) 32: 15018-15028.

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.