Quantifying and Visualizing Uncertainties in Molecular Models

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Rasheed, Muhibur; Clement, Nathan; Bhowmick, Abhishek; Bajaj, Chandrajit;
(2015)
  • Subject: Computer Science - Computational Engineering, Finance, and Science | F.2 | G.3 | 62, 65, 68

Computational molecular modeling and visualization has seen significant progress in recent years with sev- eral molecular modeling and visualization software systems in use today. Nevertheless the molecular biology community lacks techniques and tools for the rigorous a... View more
  • References (46)
    46 references, page 1 of 5

    [1] K Azuma. Weighted sums of certain dependent random variables. Tokuku Mathematical Journal, 19:357- 367, 1967.

    [2] C. Bajaj, A. Bhowmick, E. Chattopadhyay, D. Zuckerman. On Low Discrepancy Samplings in Product Spaces of Motion Groups. arXiv preprint, arXiv:1411.7753, 2014.

    [3] C. Bajaj, S.-C. Chen, and A. Rand. An efficient higher-order fast multipole boundary element solution for Poisson-Boltzmann based molecular electrostatics. SIAM J. Sci. Comput., 33(2):826-848, 2011.

    [4] C. Bajaj, P. Djeu, V. Siddavanahalli, and A. Thane. TexMol: Interactive visual exploration of large flexible multi-component molecular complexes. In Proc. IEEE Visual. Conf., pages 243-250, Austin, Texas, 2004.

    [5] C. Bajaj, H. Lee, R. Merkert, and V. Pascucci. NURBS based B-rep models from macromolecules and their properties. In Proc. Symp. Solid Model. Appl., pages 217-228, 1997.

    [6] C. Bajaj, V. Pascucci, A. Shamir, R. Holt, and A. Netravali. Dynamic maintenance and visualization of molecular surfaces. Discrete Appl. Math., 127:23-51, 2003.

    [7] C. Bajaj and R. Chowdhury and V. Siddavanahalli. F2Dock: A Fast and Fourier Based Error-Bounded Approach to Protein-Protein Docking. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(1):45-58, 2011

    [8] C. Bajaj and W. Zhao. Fast molecular solvation energetics and forces computation. SIAM J. Sci. Comput., 31(6):4524-4552, 2010.

    [9] D. Bashford and D. A. Case. Generalized Born models of macromolecular solvation effects. Annu. Rev. Phys. Chem., 51:129-152, 2000.

    [10] George EP Box and Mervin E Muller. A note on the generation of random normal deviates. The annals of mathematical statistics, 29(2):610-611, 1958.

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