Yang Shen | Publications

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.

Yang Shen [ Home \| Research \| Publications \| CAPRI \| CV \| Links ]

Software 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 You and Y Shen* (2022) Cross-Modality and Self-Supervised Protein Embedding for Compound-Protein Affinity and Contact Prediction. Bioinformatics 38(Supplement_2): ii68-ii74. Y You, Y Cao, T Chen, Z Wang and Y Shen* (2022) Bayesian Modeling and Uncertainty Quantification for Learning to Optimize: What, Why, and How. International Conference on Learning Representations (ICLR 2022) Y Cao, P Das, V Chenthamarakshan, P-Y Chen, I Melnyk and Y Shen (2021) Fold2Seq: A Joint Sequence (1D)-Fold (3D) Embedding-based Generative Model for Protein Design. Proceedings of the 38th International Conference on Machine Learning (ICML 2021) 139: 1261-1271. Y You, T Chen, Z Wang and Y Shen (2021) Graph Contrastive Learning Automated. Proceedings of the 38th International Conference on Machine Learning (ICML 2021) 139: 12121-12132. M Karimi, S Zhu, Y Cao, and Y Shen* (2020) De Novo Protein Design for Novel Folds using Guided Conditional Wasserstein Generative Adversarial Networks . Journal of Chemical Information and Modeling (cover article) 60(12): 5667-5681. M Karimi, A Hasanzadeh and Y Shen* (2020) Network-Principled Deep Generative Models for Designing Drug Combinations as Graph Sets. Bioinformatics 36(Supplement_1): i445-i454. Y You, T Chen, Y Sui, T Chen, Z Wang and Y Shen* (2020) Graph Contrastive Learning with Augmentations. Advances in Neural Information Processing Systems (NeurIPS 2020) 33: 5812-5823. Y You, T Chen, Z Wang and Y Shen (2020) When Does Self-Supervision Help Graph Convolutional Networks?. Proceedings of the 36th International Conference on Machine Learning (ICML 2020) 119: 10871-10880. Y Cao and Y Shen* (2020) Bayesian Active Learning for Optimization and Uncertainty Quantification in Protein Docking. Journal of Chemical Theory and Computation 16(8): 5334-5347. 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. Y Cao, Y Sun, M Karimi, H Chen, O Moronfoye and Y Shen* (2019) Predicting Pathogenicity of Missense Variants with Weakly Supervised Regression. Human Mutation 40(9): 1579-1592. M Karimi, D Wu, Z Wang and Y Shen* (2019) DeepAffinity: Interpretable Deep Learning of Compound-Protein Affinity through Unified Recurrent and Convolutional Neural Networks. Bioinformatics 35(18): 3329-3338. JC Kang, W Sun, P Khare, M Karimi, X Wang, Y Shen, RJ Ober and ES Ward (2019) Engineering a HER2-Specific Antibody-Drug Conjugate to Increase Lysosomal Delivery and Therapeutic Efficacy. Nature Biotechnology 37: 523-526. Highlighted in TAMU Research Bulletin, Engineering News, and Health Science Center News. M Karimi and Y Shen* (2018) iCFN: An Efficient Exact Algorithm for Multistate Protein Design. Bioinformatics 34(18): i811-i820. H Chen^, Y Sun^ and Y Shen* (2017) Predicting Protein Conformational Changes for Unbound and Homology Docking: Learning from Intrinsic and Induced Flexibility. Proteins: Structure, Function, and Bioinformatics 85(3): 544–556. T Oliwa and Y Shen* (2015) cNMA: A Framework of Encounter Complex-based Normal Mode Analysis to Model Conformational Changes in Protein Interactions. Bioinformatics 31(12): i151–i160. Y Shen, ML Radhakrishnan, and B Tidor (2015) Molecular Mechanisms and Design Principles for Promiscuous Inhibitors to Avoid Drug Resistance: Lessons Learned from HIV-1 Protease Inhibition. Proteins: Structure, Function and Bioinformatics 83(2): 351–372. Y Shen* (2013) Improved Flexible Refinement of Protein Docking in CAPRI Rounds 22-27. Proteins: Structure, Function and Bioinformatics 81(12): 2129–2136. W Toy, Y Shen, H Won, B Green, RA Sakr, M Will, Z Li, K Gala, S Fanning, TA King, C Hudis, D Chen, T Taran, G Hortobagyi, GL Greene, M Berger, J Baselga, and S Chandarlapaty (2013) ESR1 Ligand-Binding Domain Mutations in Hormone-Resistant Breast Cancer. Nature Genetics 45(12): 1439–1445. Y Shen, MD Altman, A Ali, MNL Nalam, H Cao, TM Rana, CA Schiffer, and B Tidor (2013) Testing the Substrate-Envelope Hypothesis with Designed Pairs of Compounds. ACS Chemical Biology 8(11): 2433–2441. MD Balbas, MJ Evans, DJ Hosfield, J Wongvipat, VK Arora, PA Watson, Y Chen, GL Greene, Y Shen, CL Sawyers (2013) Overcoming Mutation-Based Resistance to Antiandrogens with Rational Drug Design. eLife 2: e00499. Y Shen, MK Gilson, and B Tidor (2012) Charge Optimization Theory for Induced-Fit Ligands. Journal of Chemical Theory and Computation 8(11): 4580–4592. Y Shen, ICh Paschalidis, P Vakili, and S Vajda (2008) Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes. PLoS Computational Biology 4(10): e1000191. ICh Paschalidis, Y Shen, P Vakili, and S Vajda (2007) SDU: A Semi-Deﬁnite Programming Based Underestimation Method for Stochastic Global Optimization in Protein Docking. IEEE Transactions on Automatic Control 52(4): 664–676. 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.