Biblio
Found 33 results
2015
Chen, Brian Y. 2015. “Conformational Sampling Reveals Amino Acids With A Steric Influence On Specificity”. Journal Of Computational Biology. Journal Of Computational Biology: accepted.
Guo, Ziyi, Juliana Hong, Katya Scheinberg, and Brian Y Chen. 2015. “Superposition Of Protein Structures Using Electrostatic Isopotentials”. Proceedings Of The Ieee International Conference On Bioinformatics And Biomedicine (Bibm 2015). Proceedings Of The Ieee International Conference On Bioinformatics And Biomedicine (Bibm 2015): in review.
2014
Guo, Ziyi, Trevor K Kuhlengel, Steven R Stinson, Seth Blumenthal, Soutir Bandyopadhyay, and Brian Y Chen. 2014. “A Flexible Volumetric Comparison Of Protein Cavities Can Reveal Patterns In Ligand Binding Specificity”. In Proceedings Of The Acm Conference On Bioinformatics, Computational Biology And Biomedicine, 445-454. Proceedings Of The Acm Conference On Bioinformatics, Computational Biology And Biomedicine. ACM.
Daniels, Zachary A, Steven R Stinson, Shenchi Tian, Evan Mulbry, and Brian Y Chen. 2014. “A Gesture-Based Interface For The Exploration And Classification Of Protein Binding Cavities”. In Proceedings Of The 2014 Workshop On Mobile Augmented Reality And Robotic Technology-Based Systems, 47–50. Proceedings Of The 2014 Workshop On Mobile Augmented Reality And Robotic Technology-Based Systems. ACM.
Chen, Ruobing, Ziyi Guo, Brian Y Chen, and Katya Scheinberg. 2014. “Methodologies And Software For Derivative-Free Optimization”. In Optimization Methods In Engineering. Optimization Methods In Engineering. in review: Society for Industrial and Applied Mathematics.
Guo, Ziyi, and Brian Y Chen. 2014. “Predicting Small Molecule Substrate Specificity For Protein Function Annotation”. In Handbook Of Computational Molecular Biology. Handbook Of Computational Molecular Biology. in review: CRC Press.
Chen, Brian Y. 2014. “Vasp-E: Specificity Annotation With A Volumetric Analysis Of Electrostatic Isopotentials”. Plos Comp Biol. Plos Comp Biol: e1003792.
2013
Godshall, Brian G, Yisheng Tang, Wenjie Yang, and Brian Y Chen. 2013. “An Aggregate Analysis Of Many Predicted Structures To Reduce Errors In Protein Structure Comparison Caused By Conformational Flexibility”. Bmc Struct Biol 13. Bmc Struct Biol: S10.
Blumenthal, Seth, Yisheng Tang, Wenjie Yang, and Brian Y Chen. 2013. “Isolating Influential Regions Of Electrostatic Focusing In Protein And Dna Structure”. Ieee/Acm Transactions On Computational Biology And Bioinformatics (Tcbb) 10. Ieee/Acm Transactions On Computational Biology And Bioinformatics (Tcbb): 1188–1198.
2012
Chen, Ruobing, Katya Scheinberg, and Brian Y Chen. 2012. “Aligning Ligand Binding Cavities By Optimizing Superposed Volume”. Proceedings (Ieee Int Conf Bioinformatics Biomed). Proceedings (Ieee Int Conf Bioinformatics Biomed): 1–5.
Godshall, Brian G, and Brian Y Chen. 2012. “Improving Accuracy In Binding Site Comparison With Homology Modeling”. Proceedings (Ieee Int Conf Bioinformatics Biomed). Proceedings (Ieee Int Conf Bioinformatics Biomed): 662–669.
Chen, Brian Y, and Soutir Bandyopadhyay. 2012. “Modeling Regionalized Volumetric Differences In Protein-Ligand Binding Cavities”. Proteome Sci 10. Proteome Sci: S6.
Chen, Brian Y, and Soutir Bandyopadhyay. 2012. “A Regionalizable Statistical Model Of Intersecting Regions In Protein-Ligand Binding Cavities”. J Bioinform Comput Biol 10. J Bioinform Comput Biol.
Chen, Brian Y, and Debdas Paul. 2012. “A Volumetric Method For Representing And Comparing Regions Of Electrostatic Focusing In Molecular Structure”. In Proceedings Of The Acm Conference On Bioinformatics, Computational Biology And Biomedicine, 242–249. Proceedings Of The Acm Conference On Bioinformatics, Computational Biology And Biomedicine. ACM.
2011
Fischer, Markus, Qiangfeng Zhang, Fabian Dey, Brian Y Chen, Barry Honig, and Donald Petrey. 2011. “Markus: A Server To Navigate Sequence-Structure-Function Space.”. Nucleic Acids Res. Nucleic Acids Res: 1–5. doi:10.1093/nar/gkr468.
Chen, Brian Y, and Soutir Bandyopadhyay. 2011. “A Statistical Model Of Overlapping Volume In Ligand Binding Cavities”. In Proceedings Of The Computational Structural Bioinformatics Workshop (Csbw 2011), 424-31. Proceedings Of The Computational Structural Bioinformatics Workshop (Csbw 2011).
Chen, Brian Y, and Soutir Bandyopadhyay. 2011. “Vasp-S: A Volumetric Analysis And Statistical Model For Predicting Steric Influences On Protein-Ligand Binding Specificity”. Proceedings (Ieee Int Conf Bioinformatics Biomed). Proceedings (Ieee Int Conf Bioinformatics Biomed): 22-9.
2010
Bryant, Drew H, M Moll, Brian Y Chen, Viacheslav Y Fofanov, and Lydia E Kavraki. 2010. “Analysis Of Substructural Variation In Families Of Enzymatic Proteins With Applications To Protein Function Prediction”. Bmc Bioinformatics 11. Bmc Bioinformatics. doi:10.1186/1471-2105-11-242.
C. Andersson, David, Brian Y Chen, and Anna Linusson. 2010. “Mapping Of Ligand-Binding Cavities In Proteins.”. Proteins: Structure, Function And Bioinformatics 78. Proteins: Structure, Function And Bioinformatics: 1408–22. doi:10.1002/prot.22655.
C. Andersson, David, Brian Y Chen, and Anna Linusson. 2010. “Multivariate Assessment Of Virtual Screening Experiments”. Journal Of Chemometrics 24. Journal Of Chemometrics: 757–767. doi:10.1002/cem.1367.
Chen, Brian Y, and Barry Honig. 2010. “Vasp: A Volumetric Analysis Of Surface Properties Yields Insights Into Protein-Ligand Binding Specificity”. Plos Comput Biol 6. Plos Comput Biol: 11.
2008
Kristensen, David M, RM Ward, Andreas M Lisewski, Serkan Erdin, Brian Y Chen, Viacheslav Y Fofanov, Marek Kimmel, Lydia E Kavraki, and Olivier Lichtarge. 2008. “Prediction Of Enzyme Function Based On 3D Templates Of Evolutionarily Important Amino Acids.”. Bmc Bioinformatics 9. Bmc Bioinformatics: 17. doi:10.1186/1471-2105-9-17.
Fofanov, Viacheslav Y, Brian Y Chen, Drew H Bryant, Mark Moll, Olivier Lichtarge, Lydia E Kavraki, and Marek Kimmel. 2008. “A Statistical Model To Correct Systematic Bias Introduced By Algorithmic Thresholds In Protein Structural Comparison Algorithms”. 2008 Ieee International Conference On Bioinformatics And Biomeidcine Workshops. 2008 Ieee International Conference On Bioinformatics And Biomeidcine Workshops: 1–8. doi:10.1109/BIBMW.2008.4686202.
2007
Chen, Brian Y, Drew H Bryant, Viacheslav Y Fofanov, David M Kristensen, Amanda E Cruess, Marek Kimmel, Olivier Lichtarge, and Lydia E Kavraki. 2007. “Cavity Scaling: Automated Refinement Of Cavity-Aware Motifs In Protein Function Prediction.”. J Bioinform Comput Biol 5. J Bioinform Comput Biol: 353–82.
Chen, Brian Y, Drew H Bryant, Amanda E Cruess, JH Bylund, Viacheslav Y Fofanov, David M Kristensen, Marek Kimmel, Olivier Lichtarge, and Lydia E Kavraki. 2007. “Composite Motifs Integrating Multiple Protein Structures Increase Sensitivity For Function Prediction.”. In Computational Systems Bioinformatics Conference (Csb2007), 6:343–55. Computational Systems Bioinformatics Conference (Csb2007).