Publications

  • Journal

    • Muhibur Rasheed, R. Bettadapura, and Chandrajit Bajaj. X-ray, Cryo-EM, and computationaly predicted protein structures used in integrative modeling of HIV Env glycoprotein gp120 in complex with CD4 and 17b. Elsevier Data in Brief, 2016. DOI: 10.1016/j.dib.2016.01.001

    • Muhibur Rasheed, R. Bettadapura, and Chandrajit Bajaj. Computational refinement and validation protocol for proteins with large variable regions applied to model HIV Env spike in CD4 and 17b bound state. Structure 2015; 23(6):1138-1149. (link, pre-print and supplement)

    • Radhakrishna Bettadapura, Muhibur Rasheed, Antje Volrath, and Chandrajit Bajaj. PF2Fit: Polar fast Fourier alignment of atomistic structures with 3D electron microscopy. PLoS Computational Biology, 2015; 11(10):e1004289. doi: 10.1371/journal.pcbi.1004289. (link)

    • Rezaul Chowdhury, Muhibur Rasheed, Donald Keidel, Maysam Moussalem, Arthur Olson, Michel Sanner, and Chandrajit Bajaj, Protein-Protein Docking with F2Dock 2.0 and GB-rerank, PLoS One, 2013. (link)

    • Chandrajit Bajaj, Rezaul Alam Chowdhury and Muhibur Rasheed, A dynamic data structure for flexible molecular maintenance and informatics, Bioinformatics 2011, 27(1):55-62. (link)

  • Conference

    • Nathan Clement, Muhibur Rasheed and Chandrajit Bajaj, Uncertainty Quantified Computational Analysis of the Energetics of Virus Capsid Assembly. IEEE conference on Bioinformatics and BioMedicine, 2016 (accepted).

    • Muhibur Rasheed, Nathan Clement, Abhishek Bhowmick and Chandrajit Bajaj, Statistical Framework for Uncertainty Quantification in Computational Molecular Modeling. ACM Conference on Bioinformatics, Computational Biology and Health Informatics 2016 (link). To appear in a special issue in IEEE Transactions in Computational Biology and Bioinformatics (TCBB).

    • Muhibur Rasheed and Chandrajit Bajaj, Symmetric and highly congruent tiled meshes for shells. Proceedings of the 24th International Meshing Roundtable 2015, Procedia Engineering, 123:213-225. (link)

    • Chandrajit Bajaj, Rezaul Alam Chowdhury and Muhibur Rasheed, "A dynamic data structure for flexible molecular maintenance and informatics", ACM SPM 2009, SIAM/ACM Joint Conference on Geometric and Physical Modeling 2009:259-270. (link)

    • Muhibur Rasheed, Masud Hasan and M. Sohel Rahman, "Maximum neighbor Voronoi games", 3rd Annual Workshop on Algorithms and Computation 2009, LNCS Vol. 5431:93-104. (link)

  • PhD Dissertation

    • Muhibur Rasheed, "Predicting Multi-body Assembly of Proteins", University of Texas at Austin, Texas, USA. (link)

  • Technical Reports

      • Muhibur Rasheed and Chandrajit Bajaj, Characterization and construction of a family of highly symmetric spherical polyhedra with application in modeling self-assembling structures, arXiv:1507.08374.

      • Muhibur Rasheed, Alex Rand, and Chandrajit Bajaj. Maintaining flexible molecular surfaces using augmented dynamic octrees. Technical Report 14-23, Institute of Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX, USA (link)

    • Muhibur Rasheed and Chandrajit Bajaj. Predicting symmetric spherical shell assemblies. Technical Report 14-24, Institute of Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX, USA (link)

    • Muhibur Rasheed, Qiming Yuan, and Chandrajit Bajaj. Learning optimized scoring models for protein-protein docking. Technical Report 14-25, Institute of Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX, USA (link)

  • Under preparation (email for current version of the manuscripts)

    • Muhibur Rasheed and Chandrajit Bajaj, "Approximate and Exact Nearest Neighbor Search in Dynamic Collections of Points in High Dimensions"

    • Radhakrishna Bettadapura, Muhibur Rasheed, Antje Volrath, and Chandrajit Bajaj, "Fast Flexible Fitting using Polar FFT"

    • Muhibur Rasheed, Nathan Clement, and Chandrajit Bajaj, "Protein-protein interfaces of viral capsids"

    • Chandrajit Bajaj, Antonino Favata, Andrea Micheletti, Paolo Podio-Guidugli, Muhibur Rasheed"A multiscale comparative analysis of viral capsids' normal modes"