TY - JOUR T1 - A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation [J] AU - Li, C. AU - McGowan, M. AU - Alexov, E. AU - Zhao, S. JO - Mathematical Biosciences and Engineering PY - 2020 VL - 17 IS - 6 SP - 6259 EP - 6277 ER - TY - JOUR T1 - Modeling electrostatics in molecular biology: A tutorial of DelPhi and associated resources [Article v1. 0] AU - Panday, S. K. AU - Shashikala, M. H. AU - Koirala, M. AU - Pahari, S. AU - Chakvorty, A. AU - Peng, Y. AU - Li, L. AU - Jia, Z. AU - Li, C. AU - Alexov, E. JO - Living Journal of Computational Molecular Science PY - 2019 PB - University of Colorado Boulder VL - 1 IS - 2 SP - 10841 EP - 10841 ER - TY - JOUR T1 - DelPhi suite: New developments and review of functionalities AU - Li, C. AU - Jia, Z. AU - Chakravorty, A. AU - Pahari, S. AU - Peng, Y. AU - Basu, S. AU - Koirala, M. AU - Panday, S. K. AU - Petukh, M. AU - Li, L. AU - others, JO - Journal of computational chemistry PY - 2019 PB - John Wiley \& Sons, Inc. Hoboken, USA VL - 40 IS - 28 SP - 2502 EP - 2508 ER - TY - JOUR T1 - On the electrostatic properties of homodimeric proteins AU - Campbell, B. AU - Petukh, M. AU - Alexov, E. AU - Li, C. JO - Journal of Theoretical and Computational Chemistry PY - 2014 PB - World Scientific Publishing Company VL - 13 IS - 3 SP - 1440007 EP - 1440007 ER - TY - JOUR T1 - On the modeling of polar component of solvation energy using smooth Gaussian-based dielectric function AU - Li, L. AU - Li, C. AU - Alexov, E. JO - Journal of Theoretical and Computational Chemistry PY - 2014 PB - World Scientific Publishing Company VL - 13 IS - 3 SP - 1440002 EP - 1440002 ER - TY - CHAP T1 - Smooth dielectric function for modeling electrostatics in biological macromolecules AU - Li, L. AU - Li, C. AU - Alexov, E. TI - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY PY - 2013 VL - 246 ER - TY - JOUR T1 - Multi-Level and Interleaved Poisson-Boltzmann (MLIPB) Method for Parallel Computing of the Electrostatics and its Application in Delphi AU - Li, C. AU - Petukh, M. AU - Li, L. AU - Alexov, E. JO - Biophysical Journal PY - 2013 PB - Elsevier VL - 104 IS - 2 SP - 507a EP - 507a ER - TY - JOUR T1 - Modeling Proteins and Small Molecules with Inhomogeneous Dielectric Function: Implementation in Delphi AU - Li, L. AU - Li, C. AU - Alexov, E. JO - Biophysical Journal PY - 2013 PB - Elsevier VL - 104 IS - 2 SP - 35a EP - 35a ER - TY - JOUR T1 - Predicting non-specifically bound ions: Application to BION webserver and beryllium disease AU - Petukh, M. AU - Li, C. AU - Alexov, E. JO - Biophysical Journal PY - 2013 PB - Elsevier VL - 104 IS - 2 SP - 506a EP - 506a ER - TY - JOUR T1 - Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi AU - Li, C. AU - Petukh, M. AU - Li, L. AU - Alexov, E. JO - Journal of computational chemistry PY - 2013 PB - Wiley Online Library VL - 34 IS - 22 SP - 1949 EP - 1960 ER - TY - JOUR T1 - Progress in developing Poisson-Boltzmann equation solvers AU - Li, C. AU - Li, L. AU - Petukh, M. AU - Alexov, E. JO - Computational and Mathematical Biophysics PY - 2013 PB - De Gruyter VL - 1 IS - 1 SP - 42 EP - 62 ER - TY - JOUR T1 - On the dielectric “constant” of proteins: smooth dielectric function for macromolecular modeling and its implementation in DelPhi AU - Li, L. AU - Li, C. AU - Zhang, Z. AU - Alexov, E. JO - Journal of chemical theory and computation PY - 2013 PB - American Chemical Society VL - 9 IS - 4 SP - 2126 EP - 2136 ER - TY - CHAP T1 - Parallelized DelPhi: A multiprocessor Poisson-Boltzmann solver to calculate electrostatic energies of biological macromolecules AU - Li, C. AU - Li, L. AU - Alexov, E. TI - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY PY - 2012 VL - 244 ER - TY - JOUR T1 - New Parallelized DelPhi: Fast and Efficient Poisson-Boltzmann Solver to Calculate Electrostatics of Large Supramolecular Structures AU - Li, C. AU - Zhenirovskyy, M. AU - Li, L. AU - Alexov, E. JO - Biophysical Journal PY - 2012 PB - Elsevier VL - 102 IS - 3 SP - 270a EP - 270a ER - TY - CHAP T1 - Effect of non-uniform protein dielectric constant on the electrostatic energy calculations AU - Li, L. AU - Wang, L. AU - Li, C. AU - Alexov, E. TI - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY PY - 2012 VL - 244 ER - TY - JOUR T1 - Protein Nano-Object Integrator (ProNOI) for generating atomic style objects for molecular modeling AU - Smith, N. AU - Campbell, B. AU - Li, L. AU - Li, C. AU - Alexov, E. JO - BMC structural biology PY - 2012 PB - BioMed Central VL - 12 IS - 1 SP - 1 EP - 10 ER - TY - JOUR T1 - Predicting nonspecific ion binding using DelPhi AU - Petukh, M. AU - Zhenirovskyy, M. AU - Li, C. AU - Li, L. AU - Wang, L. AU - Alexov, E. JO - Biophysical journal PY - 2012 PB - Elsevier VL - 102 IS - 12 SP - 2885 EP - 2893 ER - TY - JOUR T1 - Highly efficient and exact method for parallelization of grid-based algorithms and its implementation in DelPhi AU - Li, C. AU - Li, L. AU - Zhang, J. AU - Alexov, E. JO - Journal of computational chemistry PY - 2012 PB - Wiley Online Library VL - 33 IS - 24 SP - 1960 EP - 1966 ER - TY - JOUR T1 - DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol AU - Smith, N. AU - Witham, S. AU - Sarkar, S. AU - Zhang, J. AU - Li, L. AU - Li, C. AU - Alexov, E. JO - Bioinformatics PY - 2012 PB - Oxford University Press VL - 28 IS - 12 SP - 1655 EP - 1657 ER - TY - JOUR T1 - DelPhi: a comprehensive suite for DelPhi software and associated resources AU - Li, L. AU - Li, C. AU - Sarkar, S. AU - Zhang, J. AU - Witham, S. AU - Zhang, Z. AU - Wang, L. AU - Smith, N. AU - Petukh, M. AU - Alexov, E. JO - BMC biophysics PY - 2012 PB - BioMed Central VL - 5 IS - 1 SP - 1 EP - 11 ER -