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Computational Biophysics and Bioinformatics

Professor Emil Alexov Group

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Journal Articles by L. Li

S. Sun, P. Poudel, E. Alexov, and L. Li
Electrostatics in Computational Biophysics and Its Implications for Disease Effects
International Journal of Molecular Sciences, 23(18), 10347, 2022
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S. K. Panday, M. H. Shashikala, M. Koirala, S. Pahari, A. Chakvorty, Y. Peng, L. Li, Z. Jia, et al.
Modeling electrostatics in molecular biology: A tutorial of DelPhi and associated resources [Article v1. 0]
Living Journal of Computational Molecular Science, 1(2), 10841, 2019
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Y. Peng, Y. Yang, L. Li, Z. Jia, W. Cao, and E. Alexov
DFMD: fast and effective DelPhiForce steered molecular dynamics approach to model ligand approach toward a receptor: Application to spermine synthase enzyme
Frontiers in molecular biosciences, 6, 74, 2019
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C. Li, Z. Jia, A. Chakravorty, S. Pahari, Y. Peng, S. Basu, M. Koirala, S. K. Panday, et al.
DelPhi suite: New developments and review of functionalities
Journal of computational chemistry, 40(28), 2502-2508, 2019
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N. Tajielyato, L. Li, Y. Peng, J. Alper, and E. Alexov
E-hooks provide guidance and a soft landing for the microtubule binding domain of dynein
Scientific reports, 8(1), 1-10, 2018
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Z. Jia, L. Li, Y. Peng, F. Ding, and E. Alexov
The capricious electrostatic force: Revealing the signaling pathway in integrin α 2-I domain
Journal of Theoretical and Computational Chemistry, 17(3), 1840001, 2018
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S. C. Godar, H. Lovelace, J. Eller, M. Spencer, L. Li, G. Hamilton, H. Sanabria, E. Alexov, et al.
Single Molecule Study of Long-Range Electrostatic Binding Affinity of Cytoplasmic Dynein's Microtubule Binding Domain
Biophysical Journal, 114(3), 512a, 2018
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A. Chakravorty, Z. Jia, L. Li, S. Zhao, and E. Alexov
Reproducing the ensemble average polar solvation energy of a protein from a single structure: gaussian-based smooth dielectric function for macromolecular modeling
Journal of chemical theory and computation, 14(2), 1020-1032, 2018
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Y. Peng, L. Sun, Z. Jia, L. Li, and E. Alexov
Predicting protein--DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver
Bioinformatics, 34(5), 779-786, 2018
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L. Li, Z. Jia, Y. Peng, S. Godar, I. Getov, S. Teng, J. Alper, and E. Alexov
Forces and Disease: Electrostatic force differences caused by mutations in kinesin motor domains can distinguish between disease-causing and non-disease-causing mutations
Scientific reports, 7(1), 1-12, 2017
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L. Li, Z. Jia, Y. Peng, A. Chakravorty, L. Sun, and E. Alexov
DelPhiForce web server: electrostatic forces and energy calculations and visualization
Bioinformatics, 33(22), 3661-3663, 2017
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L. Hoffman, L. Li, E. Alexov, H. Sanabria, and M. N. Waxham
Cytoskeletal-like Filaments of Ca2+-Calmodulin-Dependent Protein Kinase II Are Formed in a Regulated and Zn2+-Dependent Manner
Biochemistry, 56(15), 2149-2160, 2017
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A. Chakravorty, Z. Jia, L. Li, and E. Alexov
A new DelPhi feature for modeling electrostatic potential around proteins: Role of bound ions and implications for zeta-potential
Langmuir, 33(9), 2283-2295, 2017
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L. Hoffman, L. Li, E. Alexov, M. N. Waxham, and H. Sanabria
Calcium Calmodulin Regulates Zinc Mediated Changes in the Structure, Self-Association, and Activity of CaMKII
Biophysical Journal, 112(3), 444a-445a, 2017
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L. Li, J. Alper, and E. Alexov
Multi-Scale Investigation on the Mechanisms of Dyneins’ Motion on Microtubule
Biophysical Journal, 112(3), 261a, 2017
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L. Li, A. Chakravorty, and E. Alexov
DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding
Journal of computational chemistry, 38(9), 584-593, 2017
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B. Campbell, L. Li, and E. Alexov
Dielectric Properties of Biological Macromolecules and Biomolecule--Water Interfaces
Encyclopedia of Biocolloid and Biointerface Science 2V Set, 380-390, 2016
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A. Chakavorty, L. Li, and E. Alexov
Electrostatic component of binding energy: interpreting predictions from poisson--boltzmann equation and modeling protocols
Journal of computational chemistry, 37(28), 2495-2507, 2016
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L. Li, J. Alper, and E. Alexov
Cytoplasmic dynein binding, run length, and velocity are guided by long-range electrostatic interactions
Scientific reports, 6(1), 1-12, 2016
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L. Li, J. Alper, and E. Alexov
Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules
Scientific reports, 6(1), 1-12, 2016
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L. Li, L. Wang, and E. Alexov
On the energy components governing molecular recognition in the framework of continuum approaches
Frontiers in molecular biosciences, 2, 5, 2015
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L. Wang, L. Li, and E. Alexov
pKa predictions for proteins, RNA s, and DNA s with the Gaussian dielectric function using DelPhi pKa
Proteins: Structure, Function, and Bioinformatics, 83(12), 2186-2197, 2015
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T. G. Kucukkal, M. Petukh, L. Li, and E. Alexov
Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins
Current opinion in structural biology, 32, 18-24, 2015
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P. Nedumpully-Govindan, L. Li, E. G. Alexov, M. A. Blenner, and F. Ding
Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity
Bioinformatics, 30(16), 2302-2309, 2014
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R. P. Dias, L. Li, T. A. Soares, and E. Alexov
Modeling the electrostatic potential of asymmetric lipopolysaccharide membranes: the MEMPOT algorithm implemented in DelPhi
Journal of computational chemistry, 35(19), 1418-1429, 2014
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L. Li, C. Li, and E. Alexov
On the modeling of polar component of solvation energy using smooth Gaussian-based dielectric function
Journal of Theoretical and Computational Chemistry, 13(3), 1440002, 2014
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C. Li, M. Petukh, L. Li, and E. Alexov
Multi-Level and Interleaved Poisson-Boltzmann (MLIPB) Method for Parallel Computing of the Electrostatics and its Application in Delphi
Biophysical Journal, 104(2), 507a, 2013
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L. Li, C. Li, and E. Alexov
Modeling Proteins and Small Molecules with Inhomogeneous Dielectric Function: Implementation in Delphi
Biophysical Journal, 104(2), 35a, 2013
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C. Li, M. Petukh, L. Li, and E. Alexov
Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi
Journal of computational chemistry, 34(22), 1949-1960, 2013
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L. Wang, S. Witham, Z. Zhang, L. Li, M. E. Hodsdon, and E. Alexov
In silico investigation of pH-dependence of prolactin and human growth hormone binding to human prolactin receptor
Communications in computational physics, 13(1), 207, 2013
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C. Li, L. Li, M. Petukh, and E. Alexov
Progress in developing Poisson-Boltzmann equation solvers
Computational and Mathematical Biophysics, 1(1), 42-62, 2013
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L. Li, C. Li, Z. Zhang, and E. Alexov
On the dielectric “constant” of proteins: smooth dielectric function for macromolecular modeling and its implementation in DelPhi
Journal of chemical theory and computation, 9(4), 2126-2136, 2013
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C. Li, M. Zhenirovskyy, L. Li, and E. Alexov
New Parallelized DelPhi: Fast and Efficient Poisson-Boltzmann Solver to Calculate Electrostatics of Large Supramolecular Structures
Biophysical Journal, 102(3), 270a, 2012
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N. Smith, B. Campbell, L. Li, C. Li, and E. Alexov
Protein Nano-Object Integrator (ProNOI) for generating atomic style objects for molecular modeling
BMC structural biology, 12(1), 1-10, 2012
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M. Petukh, M. Zhenirovskyy, C. Li, L. Li, L. Wang, and E. Alexov
Predicting nonspecific ion binding using DelPhi
Biophysical journal, 102(12), 2885-2893, 2012
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C. Li, L. Li, J. Zhang, and E. Alexov
Highly efficient and exact method for parallelization of grid-based algorithms and its implementation in DelPhi
Journal of computational chemistry, 33(24), 1960-1966, 2012
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N. Smith, S. Witham, S. Sarkar, J. Zhang, L. Li, C. Li, and E. Alexov
DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol
Bioinformatics, 28(12), 1655-1657, 2012
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L. Li, C. Li, S. Sarkar, J. Zhang, S. Witham, Z. Zhang, L. Wang, N. Smith, et al.
DelPhi: a comprehensive suite for DelPhi software and associated resources
BMC biophysics, 5(1), 1-11, 2012
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Conference Papers

L. Li, N. Smith, and E. Alexov
Modeling ensemble-averaged electrostatics with smooth Gaussian-based dielectric function
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2014
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L. Li, C. Li, and E. Alexov
Smooth dielectric function for modeling electrostatics in biological macromolecules
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2013
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C. Li, L. Li, and E. Alexov
Parallelized DelPhi: A multiprocessor Poisson-Boltzmann solver to calculate electrostatic energies of biological macromolecules
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2012
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L. Li, L. Wang, C. Li, and E. Alexov
Effect of non-uniform protein dielectric constant on the electrostatic energy calculations
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2012
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Patents

Z. Jia, L. Li, A. Chakravorty, and E. Alexov
Treating ion distribution with G aussian-based smooth dielectric function in DelPhi
2017
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