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Computational Biophysics and Bioinformatics

Professor Emil Alexov Group

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Journal Articles by E. Alexov


S. Wang, E. Alexov, and S. Zhao
On regularization of charge singularities in solving the Poisson-Boltzmann equation with a smooth solute-solvent boundary [J]
Mathematical Biosciences and Engineering, 18(2), 1370-1405, 2021
RIS, BibTex
G. Li, S. K. Panday, and E. Alexov
SAAFEC-SEQ: A Sequence-Based Method for Predicting the Effect of Single Point Mutations on Protein Thermodynamic Stability
International Journal of Molecular Sciences, 22(2), 606, 2021
RIS, BibTex
H. Shashikala, A. Chakravorty, S. K. Panday, and E. Alexov
BION-2: Predicting Positions of Non-Specifically Bound Ions on Protein Surface by a Gaussian-Based Treatment of Electrostatics
International Journal of Molecular Sciences, 22(1), 272, 2021
RIS, BibTex
E. Alexov and others
An Ensemble Approach to Predict the Pathogenicity of Synonymous Variants.
Genes, 11(9), 2020
RIS, BibTex
C. Li, M. McGowan, E. Alexov, and S. Zhao
A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation [J]
Mathematical Biosciences and Engineering, 17(6), 6259-6277, 2020
RIS, BibTex
S. R. Ganakammal and E. Alexov
An Ensemble Approach to Predict the Pathogenicity of Synonymous Variants
Genes, 11(9), 1102, 2020
RIS, BibTex
G. Li, S. Pahari, A. K. Murthy, S. Liang, R. Fragoza, H. Yu, and E. Alexov
SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein--protein binding affinity
Bioinformatics, 2020
RIS, BibTex
M. Koirala and E. Alexov
Ab-initio binding of barnase--barstar with DelPhiForce steered Molecular Dynamics (DFMD) approach
Journal of Theoretical and Computational Chemistry, 19(4), 2050016, 2020
RIS, BibTex
Y. Peng, R. Kelle, C. Little, E. Michonova, K. G. Kornev, and E. Alexov
pH-dependent interactions of Apolipophorin-III with a lipid disk
Journal of Computational Biophysics and Chemistry, 1-12, 2020
RIS, BibTex
S. R. Ganakammal, M. Koirala, B. Wu, and E. Alexov
In-silico analysis to identify the role of MEN1 missense mutations in breast cancer
Journal of Theoretical and Computational Chemistry, 19(6), 2041002, 2020
RIS, BibTex
R. Aprigliano, S. Bradamante, B. Mihaljevic, W. Wang, S. L. F. Martin, D. L. Bordin, M. Bosshard, N. P. Montaldo, et al.
Increased p53 signaling impairs neural differentiation causing HUWE1-promoted intellectual disabilities
bioRxiv, 2020
RIS, BibTex
S. Pahari, G. Li, A. K. Murthy, S. Liang, R. Fragoza, H. Yu, and E. Alexov
SAAMBE-3D: Predicting effect of mutations on protein--protein interactions
International journal of molecular sciences, 21(7), 2563, 2020
RIS, BibTex
A. Chakravorty, S. Panday, S. Pahari, S. Zhao, and E. Alexov
Capturing the Effects of Explicit Waters in Implicit Electrostatics Modeling: Qualitative Justification of Gaussian-Based Dielectric Models in DelPhi
Journal of chemical information and modeling, 60(4), 2229-2246, 2020
RIS, BibTex
M. Koirala and E. Alexov
Computational Analysis of Missense Mutations in Creatine Transporter Protein Associated with Creatine Deficiency Syndrome
Biophysical Journal, 118(3), 197a, 2020
RIS, BibTex
S. Wang, A. Lee, E. Alexov, and S. Zhao
A regularization approach for solving Poisson’s equation with singular charge sources and diffuse interfaces
Applied Mathematics Letters, 102, 106144, 2020
RIS, BibTex
M. Koirala and E. Alexov
Computational chemistry methods to investigate the effects caused by DNA variants linked with disease
Journal of Theoretical and Computational Chemistry, 19(6), 1930001, 2020
RIS, BibTex
S. K. Panday, M. H. Shashikala, A. Chakravorty, S. Zhao, and E. Alexov
Reproducing ensemble averaged electrostatics with Super-Gaussian-based smooth dielectric function: application to electrostatic component of binding energy of protein complexes
Communications in Information and Systems, 19(4), 2019
RIS, BibTex
S. R. Ganakammal and E. Alexov
Evaluation of performance of leading algorithms for variant pathogenicity predictions and designing a combinatory predictor method: Application to Rett syndrome variants
PeerJ, 7, e8106, 2019
RIS, BibTex
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
RIS, BibTex
B. Wu, Y. Peng, J. Eggert, and E. Alexov
Novel Genetic Markers for Early Detection of Elevated Breast Cancer Risk in Women
International journal of molecular sciences, 20(19), 4828, 2019
RIS, BibTex
H. Shashikala, A. Chakravorty, and E. Alexov
Modeling electrostatic force in protein-protein recognition
Frontiers in molecular biosciences, 6, 94, 2019
RIS, BibTex
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
RIS, BibTex
N. Tajielyato and E. Alexov
Modeling pKas of unfolded proteins to probe structural models of unfolded state
Journal of Theoretical and Computational Chemistry, 18(4), 1950020, 2019
RIS, BibTex
T. Hazra, S. A. Ullah, S. Wang, E. Alexov, and S. Zhao
A super-Gaussian Poisson--Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states
Journal of mathematical biology, 79(2), 631-672, 2019
RIS, BibTex
C. J. Spellicy, Y. Peng, L. Olewiler, S. S. Cathey, R. C. Rogers, D. Bartholomew, J. Johnson, E. Alexov, et al.
Three additional patients with EED-associated overgrowth: potential mutation hotspots identified?
Journal of human genetics, 64(6), 561-572, 2019
RIS, BibTex
N. Tajielyato and E. Alexov
Processivity vs. beating: Comparing cytoplasmic and axonemal dynein microtubule binding domain association with microtubule
International journal of molecular sciences, 20(5), 1090, 2019
RIS, BibTex
S. Pahari, L. Sun, and E. Alexov
PKAD: a database of experimentally measured pKa values of ionizable groups in proteins
Database, 2019, 2019
RIS, BibTex
M. S. H. Bosthanthirige, A. Chakravorty, and E. Alexov
Modeling Electrostatic Force in Protein-Protein Recognition
Biophysical Journal, 116(3), 46a, 2019
RIS, BibTex
A. Chakravorty, J. Higham, E. Alexov, and R. H. Henchman
New method to determine the effect of dimerization on protein flexibility from molecular dynamics simulation using structural hierarchy
Biophysical Journal, 116(3), 561a-562a, 2019
RIS, BibTex
N. Tajielyato, J. Alper, and E. Alexov
Comparative Study of Flagellar and Cytoplasmic Dyneins
Biophysical Journal, 116(3), 560a, 2019
RIS, BibTex
S. Pahari, L. Sun, and E. Alexov
Surface-Free Protocol for Computing PKA's (DelPhiPKa): Applications to Protein-Protein Interactions
Biophysical Journal, 116(3), 166a, 2019
RIS, BibTex
B. Wu, Y. Peng, J. A. Eggert, and E. Alexov
Investigating the Effects of Missense Mutations in MSH2 Gene Associated with Lynch Syndrome
Biophysical Journal, 116(3), 192a, 2019
RIS, BibTex
Y. Peng, M. Koirala, and E. Alexov
Electrostatic Force Driven Molecular Dynamics Simulations
Biophysical Journal, 116(3), 290a, 2019
RIS, BibTex
A. Chakravorty, E. Gallicchio, and E. Alexov
A grid-based algorithm in conjunction with a gaussian-based model of atoms for describing molecular geometry
Journal of computational chemistry, 40(12), 1290-1304, 2019
RIS, BibTex
Y. Peng, E. Alexov, and S. Basu
Structural perspective on revealing and altering molecular functions of genetic variants linked with diseases
International journal of molecular sciences, 20(3), 548, 2019
RIS, BibTex
Y. Peng, E. Alexov, and S. Basu
Structural Perspective on Revealing and Altering Molecular Mechanisms of Genetic Variants Linked with Diseases
2018
RIS, BibTex
S. Pahari, L. Sun, S. Basu, and E. Alexov
DelPhiPKa: Including salt in the calculations and enabling polar residues to titrate
Proteins: Structure, Function, and Bioinformatics, 86(12), 1277-1283, 2018
RIS, BibTex
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
RIS, BibTex
A. Chakravorty, Z. Jia, Y. Peng, N. Tajielyato, L. Wang, and E. Alexov
Gaussian-based smooth dielectric function: a surface-free approach for modeling macromolecular binding in solvents
Frontiers in molecular biosciences, 5, 25, 2018
RIS, BibTex
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
RIS, BibTex
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
RIS, BibTex
C. J. Spellicy, J. Norris, R. Bend, C. Bupp, P. Mester, T. Reynolds, J. Dean, Y. Peng, et al.
Key apoptotic genes APAF1 and CASP9 implicated in recurrent folate-resistant neural tube defects
European Journal of Human Genetics, 26(3), 420-427, 2018
RIS, BibTex
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
RIS, BibTex
Y. Peng, R. Myers, W. Zhang, and E. Alexov
Computational investigation of the missense mutations in DHCR7 gene associated with Smith-Lemli-Opitz syndrome
International journal of molecular sciences, 19(1), 141, 2018
RIS, BibTex
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
RIS, BibTex
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
RIS, BibTex
Y. Peng and E. Alexov
Protein Conformational Disease: Visit the Facts at a Glance
eLS, 1-7, 2017
RIS, BibTex
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
RIS, BibTex
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
RIS, BibTex
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
RIS, BibTex
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
RIS, BibTex
L. Li, J. Alper, and E. Alexov
Multi-Scale Investigation on the Mechanisms of Dyneins’ Motion on Microtubule
Biophysical Journal, 112(3), 261a, 2017
RIS, BibTex
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
RIS, BibTex
Y. Peng and E. Alexov
Computational investigation of proton transfer, p K a shifts and p H-optimum of protein--DNA and protein--RNA complexes
Proteins: Structure, Function, and Bioinformatics, 85(2), 282-295, 2017
RIS, BibTex
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
RIS, BibTex
Y. Peng and E. Alexov
Cofactors-loaded quaternary structure of lysine-specific demethylase 5C (KDM5C) protein: Computational model
Proteins: Structure, Function, and Bioinformatics, 84(12), 1797-1809, 2016
RIS, BibTex
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
RIS, BibTex
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
RIS, BibTex
Y. Yang, T. G. Kucukkal, J. Li, E. Alexov, and W. Cao
Binding analysis of methyl-CpG binding domain of MeCP2 and Rett syndrome mutations
ACS chemical biology, 11(10), 2706-2715, 2016
RIS, BibTex
M. Petukh, L. Dai, and E. Alexov
SAAMBE: webserver to predict the charge of binding free energy caused by amino acids mutations
International journal of molecular sciences, 17(4), 547, 2016
RIS, BibTex
Y. Peng, J. Norris, C. Schwartz, and E. Alexov
Revealing the effects of missense mutations causing Snyder-Robinson syndrome on the stability and dimerization of spermine synthase
International journal of molecular sciences, 17(1), 77, 2016
RIS, BibTex
I. Getov, M. Petukh, and E. Alexov
SAAFEC: predicting the effect of single point mutations on protein folding free energy using a knowledge-modified MM/PBSA approach
International journal of molecular sciences, 17(4), 512, 2016
RIS, BibTex
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
RIS, BibTex
L. Wang, M. Zhang, and E. Alexov
DelPhiPKa web server: predicting p K a of proteins, RNAs and DNAs
Bioinformatics, 32(4), 614-615, 2016
RIS, BibTex
Y. Peng and E. Alexov
Investigating the linkage between disease-causing amino acid variants and their effect on protein stability and binding
Proteins: Structure, Function, and Bioinformatics, 84(2), 232-239, 2016
RIS, BibTex
E. Alexov
Navigating through genomics data to deliver testable predictions
Human Mutation, 36(2), v-v, 2015
RIS, BibTex
M. Petukh, J. Morrison, M. Li, A. Panchenko, and E. Alexov
SAMBE: The New Webserver for Predicting the Effect of nssNP on the Protein-Protein Binding Free Energy
Biophysical Journal, 108(2), 157a-158a, 2015
RIS, BibTex
M. Petukh, M. Zhang, and E. Alexov
Statistical investigation of surface bound ions and further development of BION server to include p H and salt dependence
Journal of computational chemistry, 36(32), 2381-2393, 2015
RIS, BibTex
T. G. Kucukkal and E. Alexov
Structural, dynamical, and energetical consequences of Rett syndrome mutation R133C in MeCP2
Computational and mathematical methods in medicine, 2015, 2015
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T. G. Kucukkal, Y. Yang, O. Uvarov, W. Cao, and E. Alexov
Impact of rett syndrome mutations on MeCP2 MBD stability
Biochemistry, 54(41), 6357-6368, 2015
RIS, BibTex
Y. Peng, J. Suryadi, Y. Yang, T. G. Kucukkal, W. Cao, and E. Alexov
Mutations in the KDM5C ARID domain and their plausible association with syndromic Claes-Jensen-Type disease
International journal of molecular sciences, 16(11), 27270-27287, 2015
RIS, BibTex
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
RIS, BibTex
M. Petukh, M. Li, and E. Alexov
Predicting binding free energy change caused by point mutations with knowledge-modified MM/PBSA method
PLoS computational biology, 11(7), e1004276, 2015
RIS, BibTex
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
RIS, BibTex
M. Petukh, T. G. Kucukkal, and E. Alexov
On human disease-causing amino acid variants: Statistical study of sequence and structural patterns
Human mutation, 36(5), 524-534, 2015
RIS, BibTex
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
RIS, BibTex
Z. Zhang, V. Martiny, D. Lagorce, Y. Ikeguchi, E. Alexov, and others
Rational Design of Small-Molecule Stabilizers of Spermine Synthase Dimer by Virtual
2014
RIS, BibTex
B. Wu, J. Eggert, and E. Alexov
Molecular mechanisms underlying pathogenic missense mutations
eLS, 2014
RIS, BibTex
B. Campbell, M. Petukh, E. Alexov, and C. Li
On the electrostatic properties of homodimeric proteins
Journal of Theoretical and Computational Chemistry, 13(3), 1440007, 2014
RIS, BibTex
M. Petukh and E. Alexov
Ion binding to biological macromolecules
Asian journal of physics: an international quarterly research journal, 23(5), 735, 2014
RIS, BibTex
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
RIS, BibTex
E. Alexov
Advances in human biology: combining genetics and molecular biophysics to pave the way for personalized diagnostics and medicine
Advances in Biology, 2014, 2014
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M. Petukh, B. Wu, S. Stefl, N. Smith, D. Hyde-Volpe, L. Wang, and E. Alexov
Chronic beryllium disease: revealing the role of beryllium ion and small peptides binding to HLA-DP2
PLoS One, 9(11), e111604, 2014
RIS, BibTex
T. Kimmett, N. Smith, S. Witham, M. Petukh, S. Sarkar, and E. Alexov
ProBLM web server: protein and membrane placement and orientation package
Computational and mathematical methods in medicine, 2014, 2014
RIS, BibTex
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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Z. Zhang, V. Martiny, D. Lagorce, Y. Ikeguchi, E. Alexov, and M. A. Miteva
Rational design of small-molecule stabilizers of spermine synthase dimer by virtual screening and free energy-based approach
PLoS One, 9(10), e110884, 2014
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N. Dolzhanskaya, M. A. Gonzalez, F. Sperziani, S. Stefl, J. Messing, G. Y. Wen, E. Alexov, S. Zuchner, et al.
A novel p. Leu (381) Phe mutation in presenilin 1 is associated with very early onset and unusually fast progressing dementia as well as lysosomal inclusions typically seen in Kufs disease
Journal of Alzheimer's Disease, 39(1), 23-27, 2014
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T. G. Kucukkal, Y. Yang, S. C. Chapman, W. Cao, and E. Alexov
Computational and experimental approaches to reveal the effects of single nucleotide polymorphisms with respect to disease diagnostics
International journal of molecular sciences, 15(6), 9670-9717, 2014
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M. Li, M. Petukh, E. Alexov, and A. R. Panchenko
Predicting the impact of missense mutations on protein--protein binding affinity
Journal of chemical theory and computation, 10(4), 1770-1780, 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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E. Alexov and G.-W. Wei
Preface: Special Issue on Modeling Electrostatics in Molecular Biology (MEMB)
Communications in Computational Physics, 13(1), i-v, 2013
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Z. Zhang, A. Pegg, Y. Ikeguchi, and E. Alexov
Enhancing Human Spermine Synthase Activity by Site Directed Mutations
Biophysical Journal, 104(2), 380a, 2013
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M. Petukh, C. Li, and E. Alexov
Predicting non-specifically bound ions: Application to BION webserver and beryllium disease
Biophysical Journal, 104(2), 506a, 2013
RIS, BibTex
M. Petukh, T. Kimmet, and E. Alexov
BION web server: predicting non-specifically bound surface ions
Bioinformatics, 29(6), 805-806, 2013
RIS, BibTex
E. Alexov and M. Sternberg
Understanding molecular effects of naturally occurring genetic differences.
Journal of molecular biology, 425(21), 3911-3913, 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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Z. Zhang, S. Witham, M. Petukh, G. Moroy, M. Miteva, Y. Ikeguchi, and E. Alexov
A rational free energy-based approach to understanding and targeting disease-causing missense mutations
Journal of the American Medical Informatics Association, 20(4), 643-651, 2013
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Z. Zhang, Y. Zheng, M. Petukh, A. Pegg, Y. Ikeguchi, and E. Alexov
Enhancing human spermine synthase activity by engineered mutations
PLoS Comput Biol, 9(2), e1002924, 2013
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S. Sarkar, S. Witham, J. Zhang, M. Zhenirovskyy, W. Rocchia, and E. Alexov
DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes
Communications in computational physics, 13(1), 269, 2013
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L. Wang, Z. Zhang, W. Rocchia, and E. Alexov
Using DelPhi capabilities to mimic protein’s conformational reorganization with amino acid specific dielectric constants
Communications in computational physics, 13(1), 13, 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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Z. Zhang, J. Norris, V. Kalscheuer, T. Wood, L. Wang, C. Schwartz, E. Alexov, and H. V. Esch
A Y328C missense mutation in spermine synthase causes a mild form of Snyder--Robinson syndrome
Human molecular genetics, 22(18), 3789-3797, 2013
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M. Petukh, S. Stefl, and E. Alexov
The role of protonation states in ligand-receptor recognition and binding
Current pharmaceutical design, 19(23), 4182-4190, 2013
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S. Decherchi, J. Colmenares, C. E. Catalano, M. Spagnuolo, E. Alexov, and W. Rocchia
Between algorithm and model: different molecular surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution
Communications in computational physics, 13, 61, 2013
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A. V. Onufriev and E. Alexov
Protonation and pK changes in protein-ligand binding
Quarterly reviews of biophysics, 46(2), 181, 2013
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H. Nishi, M. Tyagi, S. Teng, B. A. Shoemaker, K. Hashimoto, E. Alexov, S. Wuchty, and A. R. Panchenko
Cancer missense mutations alter binding properties of proteins and their interaction networks
PloS one, 8(6), e66273, 2013
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S. Stefl, H. Nishi, M. Petukh, A. R. Panchenko, and E. Alexov
Molecular mechanisms of disease-causing missense mutations
Journal of molecular biology, 425(21), 3919-3936, 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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M. R. GUNNER and E. ALEXOV
CALCULATION OF ELECTROSTATIC FORCES
Molecular Modeling and Dynamics of Bioinorganic Systems, 41, 361, 2012
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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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S. Witham and E. Alexov
Modeling CLIC2-RyR Interactions and the Effect of Disease Causing Mutation
Biophysical Journal, 102(3), 456a, 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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Z. Zhang, L. Wang, Y. Gao, J. Zhang, M. Zhenirovskyy, and E. Alexov
Predicting folding free energy changes upon single point mutations
Bioinformatics, 28(5), 664-671, 2012
RIS, BibTex
K. Takano, D. Liu, P. Tarpey, E. Gallant, A. Lam, S. Witham, E. Alexov, A. Chaubey, et al.
An X-linked channelopathy with cardiomegaly due to a CLIC2 mutation enhancing ryanodine receptor channel activity
Human molecular genetics, 21(20), 4497-4507, 2012
RIS, BibTex
Z. Zhang, M. A. Miteva, L. Wang, and E. Alexov
Analyzing effects of naturally occurring missense mutations
Computational and mathematical methods in medicine, 2012, 2012
RIS, BibTex
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
RIS, BibTex
Z. Zhang, J. Norris, C. Schwartz, and E. Alexov
In Silico and In Vitro Investigations of the Mutability of Disease-Causing Missense Mutation Sites in
2011
RIS, BibTex
Z. Zhang, C. Schwartz, and E. Alexov
In Silico Investigation of Mutability of Spermine Synthase
Biophysical Journal, 100(3), 321a, 2011
RIS, BibTex
Z. Zhang, C. Schwatz, and E. Alexov
\backslashtextit \In silico\ investigation of molecular effects caused by missense mutations in creatine transporter protein
Bulletin of the American Physical Society, 56, 2011
RIS, BibTex
S. Witham, K. Takano, C. Schwartz, and E. Alexov
In Silico Investigation of a Missense Mutation in CLIC2 Associated with Intellectual Disability
Biophysical Journal, 100(3), 611a, 2011
RIS, BibTex
S. Witham, K. Talley, L. Wang, Z. Zhang, S. Sarkar, D. Gao, W. Yang, and E. Alexov
Developing hybrid approaches to predict pKa values of ionizable groups
Proteins: Structure, Function, and Bioinformatics, 79(12), 3389-3399, 2011
RIS, BibTex
S. Witham, K. Takano, C. Schwartz, and E. Alexov
A missense mutation in CLIC2 associated with intellectual disability is predicted by in silico modeling to affect protein stability and dynamics
Proteins: Structure, Function, and Bioinformatics, 79(8), 2444-2454, 2011
RIS, BibTex
R. C. Mitra, Z. Zhang, and E. Alexov
In silico modeling of pH-optimum of protein--protein binding
Proteins: Structure, Function, and Bioinformatics, 79(3), 925-936, 2011
RIS, BibTex
Z. Zhang, J. Norris, C. Schwartz, and E. Alexov
In silico and in vitro investigations of the mutability of disease-causing missense mutation sites in spermine synthase
PloS one, 6(5), e20373, 2011
RIS, BibTex
Z. Zhang, S. Witham, and E. Alexov
On the role of electrostatics in protein--protein interactions
Physical biology, 8(3), 035001, 2011
RIS, BibTex
E. Alexov, E. L. Mehler, N. Baker, A. M. Baptista, Y. Huang, F. Milletti, J. E. Nielsen, D. Farrell, et al.
Progress in the prediction of pKa values in proteins
Proteins: structure, function, and bioinformatics, 79(12), 3260-3275, 2011
RIS, BibTex
Z. Zhe, T. Shaolei, and E. Alexov
From 2010 Abstracts Issue
Biophysical Journal, 98, 1096-1098, 2010
RIS, BibTex
A. Pittman, R. Saul, A. Chaubey, E. Alexov, M. Tiemeyer, R. Steet, C. Schwartz, M. B\'en\'eteau, et al.
PMCID: PMC2695060.
Int Immunol, 22(7), 593-603, 2010
RIS, BibTex
Z. Zhe, T. Shaolei, and E. Alexov
In Silico Investigation of the Molecular Effects Caused by Missense Mutations in Spermine Sythase Gene Associated with Human Mental Retardation
Biophysical Journal, 98(3), 571a, 2010
RIS, BibTex
S. Teng, A. K. Srivastava, C. E. Schwartz, E. Alexov, and L. Wang
Structural assessment of the effects of Amino Acid Substitutions on protein stability and protein? protein interaction
International journal of computational biology and drug design, 3(4), 334-349, 2010
RIS, BibTex
K. Talley and E. Alexov
On the pH-optimum of activity and stability of proteins
Proteins: Structure, Function, and Bioinformatics, 78(12), 2699-2706, 2010
RIS, BibTex
Z. Zhang, S. Teng, L. Wang, C. E. Schwartz, and E. Alexov
Computational analysis of missense mutations causing Snyder-Robinson syndrome
Human mutation, 31(9), 1043-1049, 2010
RIS, BibTex
S. Teng, T. Madej, A. Panchenko, and E. Alexov
Modeling effects of human single nucleotide polymorphisms on protein-protein interactions.(vol 96, pg 2178, 2009)
BIOPHYSICAL JOURNAL, 96(11), 4753-4753, 2009
RIS, BibTex
S. Teng, T. Madej, A. Panchenko, and E. Alexov
Modeling effects of human single nucleotide polymorphisms on protein-protein interactions
Biophysical journal, 96(6), 2178-2188, 2009
RIS, BibTex
E. Alexov
Editorial [Protein-Protein Interactions Guest Editor: Emil Alexov]
Current pharmaceutical biotechnology, 9(2), 55-56, 2008
RIS, BibTex
K. Talley, P. Kundrotas, and E. Alexov
Modeling salt dependence of protein-protein association: Linear vs non-linear Poisson-Boltzmann equation
Commun Comput Phys, 3(5), 1071-1086, 2008
RIS, BibTex
R. Mitra, R. Shyam, I. Mitra, M. A. Miteva, and E. Alexov
Calculating the protonation states of proteins and small molecules: Implications to ligand-receptor interactions
Current computer-aided drug design, 4(3), 169-179, 2008
RIS, BibTex
M. Kosloff, E. Alexov, V. Y. Arshavsky, and B. Honig
Electrostatic and lipid anchor contributions to the interaction of transducin with membranes: mechanistic implications for activation and translocation
Journal of Biological Chemistry, 283(45), 31197-31207, 2008
RIS, BibTex
K. Talley, C. Ng, M. Shoppell, P. Kundrotas, and E. Alexov
On the electrostatic component of protein-protein binding free energy
PMC biophysics, 1(1), 1-23, 2008
RIS, BibTex
P. J. Kundrotas, M. F. Lensink, and E. Alexov
Homology-based modeling of 3D structures of protein--protein complexes using alignments of modified sequence profiles
International journal of biological macromolecules, 43(2), 198-208, 2008
RIS, BibTex
S. Teng, E. Michonova-Alexova, and E. Alexov
Approaches and resources for prediction of the effects of non-synonymous single nucleotide polymorphism on protein function and interactions
Current pharmaceutical biotechnology, 9(2), 123-133, 2008
RIS, BibTex
P. Kundrotas, P. Georgieva, A. Shosheva, P. Christova, and E. Alexov
BANMOKI: A searchable database of homology-based 3D models and their electrostatic properties of five bacterial nucleoside monophosphate kinase families
International journal of biological macromolecules, 41(1), 114-119, 2007
RIS, BibTex
M. A. Miteva, E. Alexov, and B. O. Villoutreix
Protein Structure Analysis Online
Current protocols in protein science, 50(1), 2-13, 2007
RIS, BibTex
P. Kundrotas and E. Alexov
Predicting interacting and interfacial residues using continuous sequence segments
International journal of biological macromolecules, 41(5), 615-623, 2007
RIS, BibTex
P. Kundrotas, P. Georgieva, A. Shosheva, P. Christova, and E. Alexov
Assessing the quality of the homology-modeled 3D structures from electrostatic standpoint: test on bacterial nucleoside monophosphate kinase families
Journal of bioinformatics and computational biology, 5(3), 693-715, 2007
RIS, BibTex
A. Isvoran, C. Craescu, and E. Alexov
Electrostatic control of the overall shape of calmodulin: numerical calculations
European Biophysics Journal, 36(3), 225-237, 2007
RIS, BibTex
A. Ofiteru, N. Bucurenci, E. Alexov, T. Bertrand, P. Briozzo, H. Munier-Lehmann, and A.-M. Gilles
Structural and functional consequences of single amino acid substitutions in the pyrimidine base binding pocket of Escherichia coli CMP kinase
The FEBS journal, 274(13), 3363-3373, 2007
RIS, BibTex
K. Brock, K. Talley, K. Coley, P. Kundrotas, and E. Alexov
Optimization of electrostatic interactions in protein-protein complexes
Biophysical journal, 93(10), 3340-3352, 2007
RIS, BibTex
P. J. Kundrotas and E. Alexov
PROTCOM: searchable database of protein complexes enhanced with domain--domain structures
Nucleic Acids Research, 35(1), D575-D579, 2007
RIS, BibTex
C. Bertonati, B. Honig, and E. Alexov
Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies
Biophysical journal, 92(6), 1891-1899, 2007
RIS, BibTex
C. L. Tang, E. Alexov, A. M. Pyle, and B. Honig
Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides
Journal of molecular biology, 366(5), 1475-1496, 2007
RIS, BibTex
P. J. Kundrotas and E. Alexov
Predicting 3D structures of transient protein--protein complexes by homology
Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 1764(9), 1498-1511, 2006
RIS, BibTex
P. J. Kundrotas and E. G. Alexov
Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives
BMC bioinformatics, 7(1), 1-9, 2006
RIS, BibTex
P. J. Kundrotas and E. Alexov
Electrostatic properties of protein-protein complexes
Biophysical journal, 91(5), 1724-1736, 2006
RIS, BibTex
M. J. Grey, Y. Tang, E. Alexov, C. J. McKnight, D. P. Raleigh, and A. G. Palmer III
Characterizing a partially folded intermediate of the villin headpiece domain under non-denaturing conditions: contribution of His41 to the pH-dependent stability of the N-terminal subdomain
Journal of molecular biology, 355(5), 1078-1094, 2006
RIS, BibTex
Y. Wu, J. S. Hudson, Q. Lu, J. M. Moore, A. S. Mount, A. M. Rao, E. Alexov, and P. C. Ke
Coating single-walled carbon nanotubes with phospholipids
The Journal of Physical Chemistry B, 110(6), 2475-2478, 2006
RIS, BibTex
A. Shosheva, A. Donchev, M. Dimitrov, G. Kostov, G. Toromanov, V. Getov, and E. Alexov
Comparative study of the stability of poplar plastocyanin isoforms
Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 1748(1), 116-127, 2005
RIS, BibTex
J. Zhu, E. Alexov, and B. Honig
Comparative study of generalized Born models: Born radii and peptide folding
The Journal of Physical Chemistry B, 109(7), 3008-3022, 2005
RIS, BibTex
E. Alexov and M. Gunner
Modeling the First Electron Transfer from QA to QB
Molecular Bioenergetics: Simulations of Electron, Proton, and Energy Transfer, 93, 2004
RIS, BibTex
A. Shosheva, A. Donchev, M. Dimitrov, I. Zlatanov, G. Toromanov, V. Getov, and E. Alexov
Experimental and numerical study of the poplar plastocyanin isoforms using Tyr as a probe for electrostatic similarity and dissimilarity
Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 1698(1), 67-75, 2004
RIS, BibTex
E. Alexov
Calculating proton uptake/release and binding free energy taking into account ionization and conformation changes induced by protein--inhibitor association: application to plasmepsin, cathepsin D and endothiapepsin--pepstatin complexes
Proteins: Structure, Function, and Bioinformatics, 56(3), 572-584, 2004
RIS, BibTex
E. Alexov
Numerical calculations of the pH of maximal protein stability: The effect of the sequence composition and three-dimensional structure
European Journal of Biochemistry, 271(1), 173-185, 2004
RIS, BibTex
E. Alexov
Role of the protein side-chain fluctuations on the strength of pair-wise electrostatic interactions: Comparing experimental with computed pKas
Proteins: Structure, Function, and Bioinformatics, 50(1), 94-103, 2003
RIS, BibTex
C. L. Tang, L. Xie, I. Y. Koh, S. Posy, E. Alexov, and B. Honig
On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles
Journal of molecular biology, 334(5), 1043-1062, 2003
RIS, BibTex
W. Rocchia, S. Sridharan, A. Nicholls, E. Alexov, A. Chiabrera, and B. Honig
Rapid grid-based construction of the molecular surface for both molecules and geometric objects: applications to the finite difference Poisson-Boltzmann method
J Comp Chem, 23, 128-137, 2002
RIS, BibTex
J. Tandori, P. Maroti, E. Alexov, P. Sebban, and L. Baciou
Key role of proline L209 in connecting the distant quinone pockets in the reaction center of Rhodobacter sphaeroides
Proceedings of the National Academy of Sciences, 99(10), 6702-6706, 2002
RIS, BibTex
R. E. Georgescu, E. G. Alexov, and M. R. Gunner
Combining conformational flexibility and continuum electrostatics for calculating pKas in proteins
Biophysical journal, 83(4), 1731-1748, 2002
RIS, BibTex
W. Rocchia, S. Sridharan, A. Nicholls, E. Alexov, A. Chiabrera, and B. Honig
Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects
Journal of computational chemistry, 23(1), 128-137, 2002
RIS, BibTex
W. Rocchia, E. Alexov, and B. Honig
Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions (vol 105B, pg 6507, 2001)
Journal of Physical Chemistry B, 105(28), 6754-6754, 2001
RIS, BibTex
J. Tandori, L. Baciou, E. Alexov, P. Maroti, M. Schiffer, D. K. Hanson, and P. Sebban
ACCELERATED PUBLICATIONS-Revealing the involvement of extended hydrogen bond networks in the cooperative function between distant sites in bacterial reaction centers.
Journal of Biological Chemistry, 276(49), 45513-45515, 2001
RIS, BibTex
W. Rocchia, E. Alexov, and B. Honig
ADDITIONS AND CORRECTIONS-Extending the Applicability of the Nonlinear Poisson-Boltzmann Equation: Multiple Dielectric Constants and Multivalent Ions
Journal of Physical Chemistry B-Condensed Phase, 105(28), 6754, 2001
RIS, BibTex
J. Tandori, L. Baciou, E. Alexov, P. Mar\'oti, M. Schiffer, D. K. Hanson, and P. Sebban
Revealing the involvement of extended hydrogen bond networks in the cooperative function between distant sites in bacterial reaction centers
Journal of Biological Chemistry, 276(49), 45513-45515, 2001
RIS, BibTex
W. Rocchia, E. Alexov, and B. Honig
Extending the applicability of the nonlinear Poisson- Boltzmann equation: multiple dielectric constants and multivalent ions
The Journal of Physical Chemistry B, 105(28), 6507-6514, 2001
RIS, BibTex
E. Alexov, J. Miksovska, L. Baciou, M. Schiffer, D. Hanson, P. Sebban, and M. Gunner
Modeling the effects of mutations on the free energy of the first electron transfer from QA-to QB in photosynthetic reaction centers
Biochemistry, 39(20), 5940-5952, 2000
RIS, BibTex
M. Gunner and E. Alexov
A pragmatic approach to structure based calculation of coupled proton and electron transfer in proteins
Biochimica et Biophysica Acta (BBA)-Bioenergetics, 1458(1), 63-87, 2000
RIS, BibTex
E. Alexov and M. Gunner
Calculated protein and proton motions coupled to electron transfer: electron transfer from QA-to QB in bacterial photosynthetic reaction centers
Biochemistry, 38(26), 8253-8270, 1999
RIS, BibTex
M. Miteva, E. Alexov, and B. Atanasov
Numerical simulation of aldolase tetramer stability
European biophysics journal, 28(1), 67-73, 1998
RIS, BibTex
M. Gunner, E. Alexov, E. Torres, and S. Lipovaca
The importance of the protein in controlling the electrochemistry of heme metalloproteins: methods of calculation and analysis
JBIC Journal of Biological Inorganic Chemistry, 2(1), 126-134, 1997
RIS, BibTex
E. Alexov and M. Gunner
Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties
Biophysical journal, 72(5), 2075-2093, 1997
RIS, BibTex
H. Ohshima, E. Mishonova, and E. Alexov
Electrostatic interaction between two charged spherical molecules
Biophysical chemistry, 57(23), 189-203, 1996
RIS, BibTex
E. Alexov, B. Atanasov, and T. Ueki
Anisotropic behavior of the pH dependence part of Young's modulus in a lysozyme triclinic crystal
Biopolymers: Original Research on Biomolecules, 35(5), 513-522, 1995
RIS, BibTex
E. Alexov
High-Frequency Backward Waves in Longitudinally Magnetized Gyrotropic Waveguides
Contributions to Plasma Physics, 35(1), 23-32, 1995
RIS, BibTex
E. Alexov and B. Atanasov
Selective absorption of radio frequency energy due to collective motion of charged domains: case of lysozyme crystal
Journal of Biomolecular Structure and Dynamics, 13(2), 219-228, 1995
RIS, BibTex
S. Ivanov and E. Alexov
Cherenkov generation of Rayleigh electromagnetic wave in a gyrotropic plasma waveguide
Nuclear Instruments and Methods in Physics Research A, 341(1), ABS109-ABS110, 1994
RIS, BibTex
E. Alexov and E. Mishonova
Modeling of the electrostatic potential created by a spherical molecule
Journal of Macromolecular Science, Part B, 33(1), 21-35, 1994
RIS, BibTex
E. Alexov and B. Atanasov
Analysis of electrostatic interactions in ribonuclease A monoclinic crystal
Biochimica et Biophysica Acta (BBA)-Protein Structure and Molecular Enzymology, 1206(1), 55-62, 1994
RIS, BibTex
E. G. Alexov, S. T. Ivanov, and M. I. Kapchinskii
Rejection band in waveguide filled with cold magnetoactive plasma
Japanese journal of applied physics, 33(5), 2730, 1994
RIS, BibTex
S. T. Ivanov, K. Ivanova, and E. Alexov
Polaritons along the interface between an anisotropic semiconductor and a metallic screen
Physica Scripta, 49(2), 228, 1994
RIS, BibTex
S. Ivanov, K. Ivanova, and E. Alexov
Rayleigh surface waves along the boundary between a plasma and a metallic screen
Journal of plasma physics, 49(2), 227-235, 1993
RIS, BibTex
E. G. Alexov and S. T. Ivanov
Nonreciprocal effects in a plasma waveguide
IEEE transactions on plasma science, 21(2), 254-257, 1993
RIS, BibTex
E. Alexov
An additional solution of the waveguide problem for a waveguide partially filled with a magnetoactive semiconductor plasma
Physica Scripta, 46(5), 429, 1992
RIS, BibTex
E. Alexov and S. Ivanov
Anisotropic TEM-mode in a plasma waveguide
Sov. J. Plasma Phys.(USA), 16, 283, 1990
RIS, BibTex
S. Ivanov, E. Alexov, A. Bogdanov, and P. Malinov
Surface wave evolution in a waveguide with an axial plasma column upon changing the external magnetic field
Plasma physics and controlled fusion, 32(10), 791, 1990
RIS, BibTex
S. Ivanov and E. Alexov
Electromagnetic waves in waveguide partially filled with semiconductor plasma
Contributions to Plasma Physics, 30(6), 763-774, 1990
RIS, BibTex
S. Ivanov, E. Alexov, and P. Malinov
Waveguide partially filled with semiconductor plasma
Physica Scripta, 42(4), 452, 1990
RIS, BibTex
S. Ivanov, E. Alexov, and P. Malinov
Nonsymmetrical Electromagnetic Waves in Partially Plasma—Filled Waveguide
Contributions to Plasma Physics, 30(6), 755-762, 1990
RIS, BibTex
S. Ivanov, A. Bogdanov, and E. Alexov
A new family of electromagnetic waves in a waveguide filled with magnetoactive semiconductor plasma
Physica Scripta, 42(4), 458, 1990
RIS, BibTex
S. Ivanov and E. Alexov
Electromagnetic waves in a plasma waveguide
Journal of plasma Physics, 43(1), 51-67, 1990
RIS, BibTex
S. Ivanov and E. Alexov
Electromagnetic waven in fully-filled plasma waveguide
J. of Plasma, 15, 1131-1131, 1989
RIS, BibTex
S. Ivanov and E. Alexov
Electromagnetic waves in the semiconductor plasma waveguide
Physica Scripta, 40(1), 58, 1989
RIS, BibTex
S. Ivanov, E. Alexov, and P. Malinov
Symmetrical electromagnetic waves in partially-filled plasma waveguide
Plasma physics and controlled fusion, 31(6), 941, 1989
RIS, BibTex

Conference Papers


S. Pahari and E. Alexov
Modeling pKa without solute-water boundary: DelPhiPKa and its applications to protein-protein binding
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2019
RIS, BibTex
A. Chakravorty, J. Higham, E. Alexov, and R. Henchman
Effect of water on the entropy of protein-protein binding
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2019
RIS, BibTex
N. Tajielyato, J. Alper, and E. Alexov
Modeling Tubulin E-Hooks Interactions with Dynein Microtubule Binding Domain
PROTEIN SCIENCE, 2018
RIS, BibTex
Z. Jia and E. Alexov
Simulation study of integrin alpha-2 I domain activation
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2017
RIS, BibTex
Y. Peng and E. Alexov
Predicting binding free energy change caused by missense mutations in protein-DNA interactions using modified MM/PBSA method
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2017
RIS, BibTex
E. Alexov
Parallelization schemes for solving Poisson-Boltzmann equation via finite-difference method: Implementations in DelPhi and applications
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2016
RIS, BibTex
I. Getov, M. Petukh, and E. Alexov
Predicting folding free energy changes caused by single point mutations via combined usage of MM-PBSA method and biophysical characteristics
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2015
RIS, BibTex
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
RIS, BibTex
E. Alexov
Electrostatics and polarization effects in biophysical chemistry: In silico, in vitro, and in vivo
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2013
RIS, BibTex
M. Petukh, A. Panchenko, and E. Alexov
Electrostatics plays significant role in changes of the protein-protein affinity due to missense mutations
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2013
RIS, BibTex
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
RIS, BibTex
K. Vaidyanathan, T. Niranjan, M. May, R. Rose, C. F. Teo, S. Prabakaran, R. Bridger, E. Alexov, et al.
Characterizing a missense mutation in O-GlcNAc transferase that segregates with disease in a family with X-linked Intellectual Disability
GLYCOBIOLOGY, 2013
RIS, BibTex
Z. Zhang, V. Martiny, D. Lagorce, E. Alexov, M. Miteva, and others
Snyder-Robinson Syndrome: Rescuing the Disease-Causing Effect of G56S mutant by Small Molecule Binding
APS March Meeting Abstracts, 2013
RIS, BibTex
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
RIS, BibTex
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
RIS, BibTex
Z. Zhang, C. Schwatz, and E. Alexov
In silico investigation of molecular effects caused by missense mutations in creatine transporter protein
APS March Meeting Abstracts, 2011
RIS, BibTex
L. Wang, S. Sarhar, W. Rocchia, and E. Alexov
Using DelPhi capabilities to mimic conformational reorganization with amino acid specific dielectric constants
APS March Meeting Abstracts, 2011
RIS, BibTex
S. Witham, B. Boylen, B. Owesen, W. Rocchia, and E. Alexov
DelPhi webserver: Comprehensive suite for electrostatic calculations of biological macromolecules and their complexes
APS March Meeting Abstracts, 2011
RIS, BibTex
E. Alexov and B. Honig
Structural and Energetic Basis of Molecular Recognition
Handbook of Cell Signaling, Academic Press, 2010
RIS, BibTex
R. Mitra, R. Shyam, and E. Alexov
Modeling Ionization Events iduced by Protein Protein Binding
APS Southeastern Section Meeting Abstracts, 2009
RIS, BibTex
I. Mitra and E. Alexov
Multivariate Analysis of Conformational Changes Induced by Macromolecular Interactions
APS Southeastern Section Meeting Abstracts, 2009
RIS, BibTex
R. Shyam and E. Alexov
Accessing the limits of ab initio docking methods
APS Southeastern Section Meeting Abstracts, 2009
RIS, BibTex
Z. Zhang, S. Teng, and E. Alexov
Computational Modeling of Molecular Effects of Mutations Causing Snyder-Robinson Syndrome
APS Southeastern Section Meeting Abstracts, 2009
RIS, BibTex
E. Alexov, K. Brock, and P. Kundrotas
Optimization of the electrostatic interactions in protein-protein complexes
APS March Meeting Abstracts, 2007
RIS, BibTex
E. G. Alexov
Modeling protein-protein interactions with continuum electrostatics
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2007
RIS, BibTex
P. Kundrotas and E. Alexov
Utilizing Profile-to-Profile Alignments for Predicting Protein-Protein Interactions
APS March Meeting Abstracts, 2007
RIS, BibTex
P. Kundrotas and E. Alexov
Predicting protein-protein interactions using non-gapped interacting residue segments
BIOPHYSICAL JOURNAL, 2007
RIS, BibTex
P. Kundrotas and E. Alexov
Optimum pH for protein-protein complexes.
APS March Meeting Abstracts, 2006
RIS, BibTex
E. Alexov, A. Allardice, and P. Kundrotas
Combining biophysical and bioinformatical approaches for predicting residue's contacts.
APS March Meeting Abstracts, 2006
RIS, BibTex
P. Kundrotas and E. Alexov
Predicting 3D structures of transient protein-protein complexes
APS March Meeting Abstracts, 2006
RIS, BibTex
E. Alexov and M. Gunner
Modeling the First Electron Transfer from QA to QB in Reaction Center Proteins from Rb. sphaeroides
2004
RIS, BibTex
C. L. Tang, D. Petrey, M. Fasnacht, M. Kosloff, E. Alexov, and B. Honig
Use of limited suboptimal alignment in homology modeling
Poster presented at 8th Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2004
RIS, BibTex
E. Alexov and B. Honig
Proton uptake/release induced by protein-inhibitor association. Application to pepstatin and plasmepsin, cathepsin D and endothiapepsin complexes.
BIOPHYSICAL JOURNAL, 2003
RIS, BibTex
C. Tang, E. Alexov, A. Pyle, and B. Honig
Perturbations of pKa in RNA structures: A survey using a Monte Carlo application of the NLPB equation
BIOPHYSICAL JOURNAL, 2002
RIS, BibTex
E. Alexov and B. Honig
The origins of pH dependent effects on protein stability: Applications to proteases
Biophysical Journal, 2002
RIS, BibTex
E. Alexov, L. Baciou, M. Schiffer, P. Sebban, D. Hanson, and M. Gunner
Modeling the free energy chances due to mutations of residues with multi conformation continuum electrostatic (MCCE) method: Application to reaction center proteins
BIOPHYSICAL JOURNAL, 2000
RIS, BibTex
M. Gunner and E. Alexov
Calculating the role of the protein in proton-and electron-transfer reactions.
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2000
RIS, BibTex
M. Gunner and E. Alexov
Reorganization of the QB pocket of photosynthetic reaction centers stabilizes ionization changes.
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2000
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M. Gunner, D. Karpman, and E. Alexov
pK (a) calculations with conformational flexibility: the multi conformation continuum electrostatics procedure (MCCE)
Biophysical Journal, 2000
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E. Alexov and M. Gunner
Modeling the first electron transfer from QA to QB in reaction centers from the bacteria Rb.
Biophysical Journal, 1999
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M. Gunner and E. Alexov
Modeling motions in protiens that are coupled to electron tranfers.
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 1998
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M. R. Gunner and E. Alexov
The Role of the Protein in Modulating Cofactor Electrochemistry in Proteins: The Calculation of Electrostatic Forces
Molecular Modeling and Dynamics of Bioinorganic Systems, Springer, Dordrecht, 1997
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V. Alexandrov, E. G. Alexov, M. Andrec, A. Apostolico, A. Bhattacharya, D. J. Brooks, R. L. Cai, A. Colasanti, et al.
Participant List
Proceedings of the Tsukuba Global Carbon Cycle Workshop--Global Environment Tsukuba'95: February 1-3, 1995, Tsukuba, Japan, 1995
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Patents


E. Alexov
Towards More Biology-Oriented Papers: Name Change of the Journal of Theoretical and Computational Chemistry to Journal of Computational Biophysics and Chemistry
World Scientific Publishing Company, 2021
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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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E. Alexov and R. Luo
Electrostatics and polarization effects in biophysical chemistry: in silico and in vitro
WORLD SCIENTIFIC PUBL CO PTE LTD 5 TOH TUCK LINK, SINGAPORE 596224, SINGAPORE, 2014
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