E. Alexov

发表

Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties.

E. Alexov, M. Gunner, 1997, Biophysical journal.

On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles.

B. Honig, Lei Xie, E. Alexov, 2003, Journal of molecular biology.

Predicting the Impact of Missense Mutations on Protein–Protein Binding Affinity

A. Panchenko, E. Alexov, Minghui Li, 2014, Journal of chemical theory and computation.

Structural Perspective on Revealing and Altering Molecular Mechanisms of Genetic Variants Linked with Diseases

E. Alexov, Yunhui Peng, Sankar Basu, 2018 .

DFMD: Fast and Effective DelPhiForce Steered Molecular Dynamics Approach to Model Ligand Approach Toward a Receptor: Application to Spermine Synthase Enzyme

E. Alexov, Yunhui Peng, Ye Yang, 2019, Front. Mol. Biosci..

Optimization of electrostatic interactions in protein-protein complexes.

E. Alexov, Kelly P. Brock, P. Kundrotas, 2007, Biophysical journal.

Electrostatic properties of protein-protein complexes.

Emil Alexov, Petras J Kundrotas, E. Alexov, 2006, Biophysical journal.

Protonation and pK changes in protein–ligand binding

Emil Alexov, Alexey V. Onufriev, E. Alexov, 2013, Quarterly Reviews of Biophysics.

Molecular mechanisms of disease-causing missense mutations.

Shannon K. Stefl, A. Panchenko, E. Alexov, 2013, Journal of molecular biology.

The role of protonation states in ligand-receptor recognition and binding.

Emil Alexov, Shannon K. Stefl, Marharyta Petukh, 2013, Current pharmaceutical design.

On the electrostatic component of protein-protein binding free energy

Emil Alexov, Carmen Ng, Petras Kundrotas, 2008, PMC biophysics.

Advances in Human Biology: Combining Genetics and Molecular Biophysics to Pave the Way for Personalized Diagnostics and Medicine

Emil Alexov, E. Alexov, 2014 .

Numerical calculations of the pH of maximal protein stability. The effect of the sequence composition and three-dimensional structure.

Emil Alexov, E. Alexov, 2003, European journal of biochemistry.

Role of the protein side‐chain fluctuations on the strength of pair‐wise electrostatic interactions: Comparing experimental with computed pKas

Emil Alexov, E. Alexov, 2002, Proteins.

Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins.

E. Alexov, M. Gunner, R. Georgescu, 2002, Biophysical journal.

Computational and Experimental Approaches to Reveal the Effects of Single Nucleotide Polymorphisms with Respect to Disease Diagnostics

Tugba G. Kucukkal, E. Alexov, Ye Yang, 2014, International journal of molecular sciences.

Modeling pKas of unfolded proteins to probe structural models of unfolded state

E. Alexov, N. Tajielyato, 2019, Journal of Theoretical and Computational Chemistry.

Forces and Disease: Electrostatic force differences caused by mutations in kinesin motor domains can distinguish between disease-causing and non-disease-causing mutations

Lin Li, E. Alexov, Yunhui Peng, 2017, Scientific Reports.

Investigating the linkage between disease‐causing amino acid variants and their effect on protein stability and binding

E. Alexov, Yunhui Peng, 2016, Proteins.

SAAMBE: Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations

E. Alexov, M. Petukh, Luogeng Dai, 2016, International journal of molecular sciences.

SAAFEC: Predicting the Effect of Single Point Mutations on Protein Folding Free Energy Using a Knowledge-Modified MM/PBSA Approach

E. Alexov, M. Petukh, I. Getov, 2016, International journal of molecular sciences.

Impact of Rett Syndrome Mutations on MeCP2 MBD Stability.

Tugba G. Kucukkal, E. Alexov, Ye Yang, 2015, Biochemistry.

On Human Disease‐Causing Amino Acid Variants: Statistical Study of Sequence and Structural Patterns

Tugba G. Kucukkal, E. Alexov, M. Petukh, 2015, Human mutation.

Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins.

Tugba G. Kucukkal, Lin Li, E. Alexov, 2015, Current opinion in structural biology.

Coating single-walled carbon nanotubes with phospholipids.

A. Rao, E. Alexov, A. Mount, 2006, The journal of physical chemistry. B.

DelPhiPKa: Including salt in the calculations and enabling polar residues to titrate

E. Alexov, Sankar Basu, S. Pahari, 2018, Proteins.

Progress in the prediction of pKa values in proteins

Sarah L. Williams, Jana K. Shen, J. Warwicker, 2011, Proteins.

Approaches and resources for prediction of the effects of non-synonymous single nucleotide polymorphism on protein function and interactions.

E. Alexov, E. Michonova-Alexova, S. Teng, 2008, Current pharmaceutical biotechnology.

In Silico and In Vitro Investigations of the Mutability of Disease-Causing Missense Mutation Sites in Spermine Synthase

Zhe Zhang, C. Schwartz, E. Alexov, 2011, PloS one.

Cancer Missense Mutations Alter Binding Properties of Proteins and Their Interaction Networks

Benjamin A. Shoemaker, A. Panchenko, S. Wuchty, 2013, PloS one.

Between algorithm and model: different Molecular Surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution.

M. Spagnuolo, W. Rocchia, C. Catalano, 2013, Communications in computational physics.

An X-linked channelopathy with cardiomegaly due to a CLIC2 mutation enhancing ryanodine receptor channel activity.

Emil Alexov, Kyoko Takano, Shawn Witham, 2012, Human molecular genetics.

Hope for GWAS: Relevant Risk Genes Uncovered from GWAS Statistical Noise

C. Correia, A. Vicente, J. Pereira-Leal, 2014, International journal of molecular sciences.

pKa predictions for proteins, RNAs, and DNAs with the Gaussian dielectric function using DelPhi pKa

Lin Li, Emil Alexov, Lin Li, 2015, Proteins.

Using DelPhi capabilities to mimic protein's conformational reorganization with amino acid specific dielectric constants.

Emil Alexov, Walter Rocchia, W. Rocchia, 2013, Communications in computational physics.

In silico modeling of pH‐optimum of protein–protein binding

Emil Alexov, Rooplekha C. Mitra, E. Alexov, 2011, Proteins.

Developing hybrid approaches to predict pKa values of ionizable groups

Wei Yang, Emil Alexov, Shawn Witham, 2011, Proteins.

A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation

E. Alexov, S. Zhao, Chuan Li, 2020, Mathematical biosciences and engineering : MBE.

Rational Design of Small-Molecule Stabilizers of Spermine Synthase Dimer by Virtual Screening and Free Energy-Based Approach

Zhe Zhang, Emil Alexov, David Lagorce, 2014, PloS one.

Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies.

Emil Alexov, Barry Honig, B. Honig, 2007, Biophysical journal.

Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases

E. Alexov, Yunhui Peng, Sankar Basu, 2019, International journal of molecular sciences.

Calculated protein and proton motions coupled to electron transfer: electron transfer from QA- to QB in bacterial photosynthetic reaction centers.

E. Alexov, M. Gunner, M R Gunner, 1999, Biochemistry.

Modeling the effects of mutations on the free energy of the first electron transfer from QA- to QB in photosynthetic reaction centers.

E. Alexov, M. Gunner, M. Schiffer, 2000, Biochemistry.

Cytoskeletal-like Filaments of Ca2+-Calmodulin-Dependent Protein Kinase II Are Formed in a Regulated and Zn2+-Dependent Manner.

M. Waxham, Lin Li, E. Alexov, 2017, Biochemistry.

Protein Structure Analysis Online

E. Alexov, B. Villoutreix, M. Miteva, 2007, Current protocols in protein science.

Modeling Electrostatic Force in Protein-Protein Recognition

E. Alexov, Mihiri Shashikala Hewa Bosthanthirige, A. Chakravorty, 2019, Front. Mol. Biosci..

Modeling Electrostatic Force in Protein-Protein Recognition

E. Alexov, A. Chakravorty, H. B. M. Shashikala, 2019, Frontiers in molecular biosciences.

Reproducing the Ensemble Average Polar Solvation Energy of a Protein from a Single Structure: Gaussian-Based Smooth Dielectric Function for Macromolecular Modeling.

Lin Li, E. Alexov, Zhe Jia, 2018, Journal of chemical theory and computation.

Three additional patients with EED-associated overgrowth: potential mutation hotspots identified?

E. Alexov, M. Friez, Yunhui Peng, 2019, Journal of Human Genetics.

The capricious electrostatic force: Revealing the signaling pathway in integrin α2-I domain

E. Alexov, Yunhui Peng, Lin Li, 2018 .

Electrostatic interaction between two charged spherical molecules.

H. Ohshima, E. Alexov, E. Mishonova, 1996, Biophysical chemistry.

Novel Genetic Markers for Early Detection of Elevated Breast Cancer Risk in Women

E. Alexov, Yunhui Peng, J. Eggert, 2019, International journal of molecular sciences.

A New DelPhi Feature for Modeling Electrostatic Potential around Proteins: Role of Bound Ions and Implications for Zeta-Potential.

Lin Li, E. Alexov, Zhe Jia, 2017, Langmuir : the ACS journal of surfaces and colloids.

Dielectric Properties of Biological Macromolecules and Biomolecule–Water Interfaces

E. Alexov, Lin Li, Brandon Campbell, 2016 .

A super-Gaussian Poisson–Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states

E. Alexov, Tania Hazra, Sheik Ahmed Ullah, 2019, Journal of Mathematical Biology.

Association of Nicotinamide Phosphoribosyltransferase (NAMPT) Gene Polymorphisms and of Serum NAMPT Levels with Dilated Cardiomyopathy in a Chinese Population

Bin Zhou, E. Alexov, Kui Zhang, 2015, International journal of molecular sciences.

ZC4H2, an XLID gene, is required for the generation of a specific subset of CNS interneurons

Shannon K. Stefl, Cheol‐Hee Kim, P. Tarpey, 2015, Human molecular genetics.

Electromagnetic waves in the semiconductor plasma waveguide

E. Alexov, S. Ivanov, 1989 .

An Ensemble Approach to Predict the Pathogenicity of Synonymous Variants

E. Alexov, Satishkumar Ranganathan Ganakammal, 2020, Genes.

Mutations in the KDM5C ARID Domain and Their Plausible Association with Syndromic Claes-Jensen-Type Disease

Tugba G. Kucukkal, E. Alexov, Yunhui Peng, 2015, International journal of molecular sciences.

Protein Conformational Disease: Visit the Facts at a Glance

E. Alexov, Yunhui Peng, 2017 .

In-silico analysis to identify the role of MEN1 missense mutations in breast cancer

E. Alexov, Bohua Wu, S. R. Ganakammal, 2020 .

Convergence of a diffuse interface Poisson-Boltzmann (PB) model to the sharp interface PB model: A unified regularization formulation

E. Alexov, Mark McGowan, Yuanzhen Shao, 2023, Appl. Math. Comput..

Molecular Mechanisms Underlying Pathogenic Missense Mutations

E. Alexov, J. Eggert, Bohua Wu, 2014 .

Processivity vs. Beating: Comparing Cytoplasmic and Axonemal Dynein Microtubule Binding Domain Association with Microtubule

E. Alexov, N. Tajielyato, 2019, International journal of molecular sciences.

E-hooks provide guidance and a soft landing for the microtubule binding domain of dynein

E. Alexov, Yunhui Peng, Lin Li, 2018, Scientific Reports.

Modeling electrostatics in molecular biology: A tutorial of DelPhi and associated resources [Article v1.0]

Emil Alexov, Mahesh Koirala, Shailesh Kumar Panday, 2019, Living Journal of Computational Molecular Science.

Gaussian-Based Smooth Dielectric Function: A Surface-Free Approach for Modeling Macromolecular Binding in Solvents

E. Alexov, Yunhui Peng, Zhe Jia, 2018, Front. Mol. Biosci..

Nonsymmetrical Electromagnetic Waves in Partially Plasma — Filled Waveguide

E. Alexov, P. Malinov, S. Ivanov, 1990 .

A regularization approach for solving the super-Gaussian Poisson-Boltzmann model with heterogeneous dielectric functions

E. Alexov, Yuanzhen Shao, Siwen Wang, 2022, J. Comput. Phys..

Enhancing Human Spermine Synthase Activity by Engineered Mutations

Zhe Zhang, Emil Alexov, Yueli Zheng, 2013, PLoS Comput. Biol..

Analyzing Effects of Naturally Occurring Missense Mutations

Lin Wang, Zhe Zhang, Emil Alexov, 2012, Comput. Math. Methods Medicine.

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.

D. Raleigh, A. Palmer, E. Alexov, 2006, Journal of molecular biology.

Experimental and numerical study of the poplar plastocyanin isoforms using Tyr as a probe for electrostatic similarity and dissimilarity.

E. Alexov, M. Dimitrov, I. Zlatanov, 2004, Biochimica et biophysica acta.

On the Dielectric “Constant” of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi

Lin Li, Emil Alexov, Zhe Zhang, 2013, Journal of chemical theory and computation.

PKAD: a database of experimentally measured pKa values of ionizable groups in proteins

Emil Alexov, Swagata Pahari, Lexuan Sun, 2019, Database J. Biol. Databases Curation.

DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes.

Emil Alexov, Jie Zhang, Walter Rocchia, 2013, Communications in computational physics.

On the pH‐optimum of activity and stability of proteins

Emil Alexov, E. Alexov, K. Talley, 2010, Proteins.

Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides.

Emil Alexov, Barry Honig, Anna Marie Pyle, 2007, Journal of molecular biology.

Identification and characterization of a missense mutation in the O-linked β-N-acetylglucosamine (O-GlcNAc) transferase gene that segregates with X-linked intellectual disability

Tao Wang, Emil Alexov, Brent Weatherly, 2017, The Journal of Biological Chemistry.

Electrostatic and Lipid Anchor Contributions to the Interaction of Transducin with Membranes

B. Honig, M. Kosloff, V. Arshavsky, 2008, Journal of Biological Chemistry.

Key role of proline L209 in connecting the distant quinone pockets in the reaction center of Rhodobacter sphaeroides

E. Alexov, P. Sebban, J. Tandori, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Computational analysis of missense mutations causing Snyder‐Robinson syndrome

Zhe Zhang, Emil Alexov, Liangjiang Wang, 2010, Human mutation.

Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling

Lei Xie, Avner Schlessinger, Emil Alexov, 2003, Proteins.

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.

Shannon K. Stefl, E. Alexov, Michael A. Gonzalez, 2014, Journal of Alzheimer's disease : JAD.

Modeling effects of human single nucleotide polymorphisms on protein-protein interactions.

Emil Alexov, Thomas Madej, Anna Panchenko, 2009, Biophysical journal.

Evaluation of performance of leading algorithms for variant pathogenicity predictions and designing a combinatory predictor method: application to Rett syndrome variants

Emil Alexov, Satishkumar Ranganathan Ganakammal, E. Alexov, 2019, PeerJ.

Computational investigation of proton transfer, pKa shifts and pH‐optimum of protein–DNA and protein–RNA complexes

E. Alexov, Yunhui Peng, 2017, Proteins.

Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy

Cheol‐Hee Kim, C. Skinner, R. Stevenson, 2020, Nature Communications.

A mutation in a ganglioside biosynthetic enzyme, ST3GAL5, results in salt & pepper syndrome, a neurocutaneous disorder with altered glycolipid and glycoprotein glycosylation.

Emil Alexov, Michael Tiemeyer, Kazuhiro Aoki, 2014, Human molecular genetics.

A Y328C missense mutation in spermine synthase causes a mild form of Snyder-Robinson syndrome.

Zhe Zhang, C. Schwartz, H. Van Esch, 2013, Human molecular genetics.

Predicting folding free energy changes upon single point mutations

Yang Gao, Lin Wang, Zhe Zhang, 2012, Bioinform..

Increased p53 signaling impairs neural differentiation in HUWE1-promoted intellectual disabilities

C. Skinner, C. Schwartz, G. Sullivan, 2021, Cell reports. Medicine.

Increased p53 signaling impairs neural differentiation causing HUWE1-promoted intellectual disabilities

C. Skinner, C. Schwartz, E. Alexov, 2020, bioRxiv.

Protein Nano-Object Integrator (ProNOI) for generating atomic style objects for molecular modeling

Lin Li, Emil Alexov, Lin Li, 2012, BMC Structural Biology.

Structural, Dynamical, and Energetical Consequences of Rett Syndrome Mutation R133C in MeCP2

Emil Alexov, Tugba G. Kucukkal, E. Alexov, 2015, Comput. Math. Methods Medicine.

Modeling the electrostatic potential of asymmetric lipopolysaccharide membranes: The MEMPOT algorithm implemented in DelPhi

Lin Li, Emil Alexov, Thereza A. Soares, 2014, J. Comput. Chem..

Structural assessment of the effects of Amino Acid Substitutions on protein stability and protein-protein interaction

Emil Alexov, Anand K. Srivastava, Liangjiang Wang, 2010, Int. J. Comput. Biol. Drug Des..

SAAFEC-SEQ: A Sequence-Based Method for Predicting the Effect of Single Point Mutations on Protein Thermodynamic Stability

Shailesh Kumar Panday, E. Alexov, Gen Li, 2021, International journal of molecular sciences.

Binding Analysis of Methyl-CpG Binding Domain of MeCP2 and Rett Syndrome Mutations.

Emil Alexov, Tugba G. Kucukkal, Jing Li, 2016, ACS chemical biology.

Cytoplasmic dynein binding, run length, and velocity are guided by long-range electrostatic interactions

Emil Alexov, E. Alexov, Lin Li, 2016, Scientific Reports.

Effects of Single-Nucleotide Polymorphisms in Calmodulin-Dependent Protein Kinase Kinase 2 (CAMKK2): A Comprehensive Study

Zoya Khalid, Omar Almaghrabi, Emil Alexov, 2020, Comput. Math. Methods Medicine.

Three additional patients with EED-associated overgrowth: potential mutation hotspots identified?

E. Alexov, M. Friez, Yunhui Peng, 2019, Journal of Human Genetics.

Predicting protein‐DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver

Lin Li, Emil Alexov, Yunhui Peng, 2018, Bioinform..

SAMPDI-3D: predicting the effects of protein and DNA mutations on protein-DNA interactions

Emil Alexov, Shailesh Kumar Panday, Yunhui Peng, 2021, Bioinform..

DelPhi: a comprehensive suite for DelPhi software and associated resources

Lin Li, Zhe Zhang, Jie Zhang, 2012, BMC biophysics.

Protein–Protein Binding Free Energy Predictions with the MM/PBSA Approach Complemented with the Gaussian-Based Method for Entropy Estimation

Shailesh Kumar Panday, E. Alexov, S. Panday, 2022, ACS omega.

Cofactors‐loaded quaternary structure of lysine‐specific demethylase 5C (KDM5C) protein: Computational model

E. Alexov, Yunhui Peng, 2016, Proteins.

Computational Investigation of the pH Dependence of Stability of Melanosome Proteins: Implication for Melanosome formation and Disease

E. Alexov, S. Loftus, Jacob Jeffries, 2021, International journal of molecular sciences.

Treating ion distribution with Gaussian‐based smooth dielectric function in DelPhi

Lin Li, Emil Alexov, Arghya Chakravorty, 2017, J. Comput. Chem..

Statistical investigation of surface bound ions and further development of BION server to include pH and salt dependence

Min Zhang, Emil Alexov, Marharyta Petukh, 2015, J. Comput. Chem..

Predicting nonspecific ion binding using DelPhi.

Emil Alexov, Lin Li, Marharyta Petukh, 2012, Biophysical journal.

Polaritons along the interface between an anisotropic semiconductor and a metallic screen

E. Alexov, S. Ivanov, K. Ivanova, 1994 .

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

Emil Alexov, Barry Honig, Anthony Nicholls, 2002, J. Comput. Chem..

Opioid Addiction and Opioid Receptor Dimerization: Structural Modeling of the OPRD1 and OPRM1 Heterodimer and Its Signaling Pathways

E. Alexov, Bohua Wu, William Hand, 2021, International journal of molecular sciences.

Selective absorption of radio frequency energy due to collective motion of charged domains: case of lysozyme crystal.

B. Atanasov, E. Alexov, Boris P. Atanasov, 1995, Journal of biomolecular structure & dynamics.

SAAMBE-3D: Predicting Effect of Mutations on Protein–Protein Interactions

Emil Alexov, Swagata Pahari, Siqi Liang, 2020, International journal of molecular sciences.

Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method

Emil Alexov, Minghui Li, Marharyta Petukh, 2015, PLoS Comput. Biol..

Comparative study of the stability of poplar plastocyanin isoforms.

E. Alexov, G. Kostov, M. Dimitrov, 2005, Biochimica et biophysica acta.

Ab-initio binding of barnase–barstar with DelPhiForce steered Molecular Dynamics (DFMD) approach

Emil Alexov, Mahesh Koirala, E. Alexov, 2020, Journal of Theoretical and Computational Chemistry.

Electrostatic control of the overall shape of calmodulin: numerical calculations

A. Isvoran, E. Alexov, A. Isvoran, 2007, European Biophysics Journal.

Highly efficient and exact method for parallelization of grid‐based algorithms and its implementation in DelPhi

Chuan Li, Lin Li, Emil Alexov, 2012, J. Comput. Chem..

On the role of electrostatics in protein–protein interactions

Zhe Zhang, Emil Alexov, Shawn Witham, 2011, Physical biology.

A pragmatic approach to structure based calculation of coupled proton and electron transfer in proteins.

E. Alexov, M. Gunner, Emil Alexov, 2000, Biochimica et biophysica acta.

Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives

Emil Alexov, Petras J. Kundrotas, E. Alexov, 2006, BMC Bioinformatics.

A new family of electromagnetic waves in a waveguide filled with magnetoactive semiconductor plasma

E. Alexov, S. Ivanov, A. Bogdanov, 1990 .

Numerical simulation of aldolase tetramer stability

B. Atanasov, E. Alexov, M. Miteva, 1998, European Biophysics Journal.

Key apoptotic genes APAF1 and CASP9 implicated in recurrent folate-resistant neural tube defects

C. Schwartz, E. Alexov, Yunhui Peng, 2018, European Journal of Human Genetics.

Structural and functional consequences of single amino acid substitutions in the pyrimidine base binding pocket of Escherichia coli CMP kinase

Emil Alexov, Thomas Bertrand, Hélène Munier-Lehmann, 2007, The FEBS journal.

Computational Investigation of the Missense Mutations in DHCR7 Gene Associated with Smith-Lemli-Opitz Syndrome

E. Alexov, Yunhui Peng, R. Myers, 2018, International journal of molecular sciences.

Analysis of electrostatic interactions in ribonuclease A monoclinic crystal.

B. Atanasov, E. Alexov, B Atanasov, 1994, Biochimica et biophysica acta.

Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules

Emil Alexov, E. Alexov, Lin Li, 2016, Scientific Reports.

On the energy components governing molecular recognition in the framework of continuum approaches

Lin Li, Lin Wang, Emil Alexov, 2015, Front. Mol. Biosci..

In silico investigation of pH-dependence of prolactin and human growth hormone binding to human prolactin receptor.

Emil Alexov, Lin Li, Shawn Witham, 2013, Communications in computational physics.

Revealing the Effects of Missense Mutations Causing Snyder-Robinson Syndrome on the Stability and Dimerization of Spermine Synthase

C. Schwartz, E. Alexov, Yunhui Peng, 2016, International journal of molecular sciences.

DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol

Chuan Li, Lin Li, Emil Alexov, 2012, Bioinform..

A grid‐based algorithm in conjunction with a gaussian‐based model of atoms for describing molecular geometry

Emil Alexov, Arghya Chakravorty, Emilio Gallicchio, 2019, J. Comput. Chem..

Comparative study of generalized born models: Born radii and peptide folding.

Emil Alexov, Barry Honig, B. Honig, 2005, The journal of physical chemistry. B.

On the linkage of thermodynamics and pathogenicity.

E. Alexov, P. Pandey, Bohua Wu, 2023, Current opinion in structural biology.

On the electrostatic properties of homodimeric proteins.

Emil Alexov, Marharyta Petukh, E. Alexov, 2014, Journal of theoretical & computational chemistry.

Electromagnetic waves in a plasma waveguide

E. Alexov, S. Ivanov, 1990, Journal of Plasma Physics.

High-frequency backward waves in longitudinally magnetized gyrotropic waveguides

E. Alexov, 1995 .

Waveguide partially filled with semiconductor plasma

E. Alexov, P. Malinov, S. Ivanov, 1990 .

Chronic Beryllium Disease: Revealing the Role of Beryllium Ion and Small Peptides Binding to HLA-DP2

Li Wang, Emil Alexov, Shannon K. Stefl, 2014, PloS one.

Progress in developing Poisson-Boltzmann equation solvers

Emil Alexov, Lin Li, Chuan Li, 2013, Molecular Based Mathematical Biology.

PROGRESS IN THE PREDICTION OF pK a VALUES IN PROTEINS

Nathan A. Baker, Emil Alexov, Damien Farrell, 2011 .

Modeling of the electrostatic potential created by a spherical molecule

E. Alexov, E. Mishonova, 1994 .

DelPhi Web Server: A Comprehensive Online Suite

Emil Alexov, Walter Rocchia, Shawn Witham, 2011 .

The Role of the Protein in Modulating Cofactor Electrochemistry in Proteins: The Calculation of Electrostatic Forces

E. Alexov, M. Gunner, 1997 .

DelPhi Suite: New Developments and Review of Functionalities

Emil Alexov, Mahesh Koirala, Arghya Chakravorty, 2019, J. Comput. Chem..

Electrostatics in Computational Biophysics and Its Implications for Disease Effects

Lin Li, E. Alexov, Shengjie Sun, 2022, International journal of molecular sciences.

pH-Dependent Interactions of Apolipophorin-III with a Lipid Disk

E. Alexov, Yunhui Peng, Ekaterina Michonova, 2020, Journal of Computational Biophysics and Chemistry.

Computational chemistry methods to investigate the effects caused by DNA variants linked with disease

Emil Alexov, Mahesh Koirala, E. Alexov, 2020, Journal of Theoretical and Computational Chemistry.

DelPhiForce web server: electrostatic forces and energy calculations and visualization

Lin Li, Emil Alexov, Arghya Chakravorty, 2017, Bioinform..

DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding

Lin Li, Emil Alexov, Arghya Chakravorty, 2017, J. Comput. Chem..

Research and applications: A rational free energy-based approach to understanding and targeting disease-causing missense mutations

Zhe Zhang, Emil Alexov, Maria A. Miteva, 2013, J. Am. Medical Informatics Assoc..

ProBLM Web Server: Protein and Membrane Placement and Orientation Package

Emil Alexov, Nicholas Smith, Marharyta Petukh, 2014, Comput. Math. Methods Medicine.

Preface: Special Issue on Modeling Electrostatics in Molecular Biology (MEMB)

Emil Alexov, Guo-Wei Wei, G. Wei, 2013 .

BION-2: Predicting Positions of Non-Specifically Bound Ions on Protein Surface by a Gaussian-Based Treatment of Electrostatics

Shailesh Kumar Panday, E. Alexov, A. Chakravorty, 2020, International journal of molecular sciences.

BION-2: Predicting Positions of Non-Specifically Bound ions on Protein Surface by a Gaussian-based Treatment of Electrostatic Environment

Mihiri H. B. Shashikala, E. Alexov, S. Pandey, 2020 .

Combining biophysical and bioinformatical approaches for predicting residue's contacts.

Emil Alexov, Amber Allardice, Petras J. Kundrotas, 2006 .

On regularization of charge singularities in solving the Poisson-Boltzmann equation with a smooth solute-solvent boundary.

E. Alexov, Siwen Wang, Shan Zhao, 2021, Mathematical biosciences and engineering : MBE.

Electrostatic component of binding energy: Interpreting predictions from poisson–boltzmann equation and modeling protocols

Lin Li, Emil Alexov, Arghya Chakravorty, 2016, J. Comput. Chem..

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

Emil Alexov, E. Alexov, 2004, Proteins.

SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein-protein binding affinity

Emil Alexov, Swagata Pahari, Haiyuan Yu, 2020, Bioinform..

A missense mutation in CLIC2 associated with intellectual disability is predicted by in silico modeling to affect protein stability and dynamics

Emil Alexov, Kyoko Takano, Shawn Witham, 2011, Proteins.

DelPhiPKa web server: predicting pKa of proteins, RNAs and DNAs

Lin Wang, Min Zhang, Emil Alexov, 2015, Bioinform..

Reproducing ensemble averaged electrostatics with Super-Gaussian-based smooth dielectric function: application to electrostatic component of binding energy of protein complexes

Emil Alexov, Arghya Chakravorty, Shailesh Kumar Panday, 2019, Commun. Inf. Syst..

Calculating the Protonation States of Proteins and Small Molecules: Implications to Ligand-Receptor Interactions

Emil Alexov, Maria A. Miteva, Radhey Shyam, 2008 .

On the Modeling of Polar Component of Solvation Energy using Smooth Gaussian-Based Dielectric Function.

Emil Alexov, Lin Li, E. Alexov, 2014, Journal of theoretical & computational chemistry.

BIOINFORMATICS DelPhi web server v2: incorporating atomic-style geometrical ﬁgures into the computational protocol

Lin Li, E. Alexov, Shawn Witham, 2012 .

Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi

Chuan Li, Lin Li, Emil Alexov, 2013, J. Comput. Chem..

BION web server: predicting non-specifically bound surface ions

Emil Alexov, Marharyta Petukh, Taylor Kimmet, 2013, Bioinform..

Editorial [ Protein-Protein Interactions Guest Editor: Emil Alexov ]

Emil Alexov, E. Alexov, 2008 .

BANMOKI: a searchable database of homology-based 3D models and their electrostatic properties of five bacterial nucleoside monophosphate kinase families.

E. Alexov, P. Kundrotas, P. Christova, 2007, International journal of biological macromolecules.

Assessing the Quality of the Homology-Modeled 3D Structures from electrostatic Standpoint: Test on bacterial nucleoside monophosphate kinase Families

Emil Alexov, Petras J. Kundrotas, Paulina Georgieva, 2007, J. Bioinform. Comput. Biol..

A regularization approach for solving Poisson's equation with singular charge sources and diffuse interfaces pdf

Emil Alexov, Siwen Wang, Shan Zhao, 2019, Appl. Math. Lett..

Capturing the Effects of Explicit Waters in Implicit Electrostatics Modeling: Qualitative Justification of Gaussian-Based Dielectric Models in DelPhi

Shan Zhao, Emil Alexov, Arghya Chakravorty, 2020, J. Chem. Inf. Model..

A super-Gaussian Poisson–Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states

E. Alexov, Tania Hazra, Sheik Ahmed Ullah, 2019, Journal of Mathematical Biology.

Ion binding to biological macromolecules.

Emil Alexov, Marharyta Petukh, E. Alexov, 2014, Asian journal of physics : an international quarterly research journal.

Revealing the Involvement of Extended Hydrogen Bond Networks in the Cooperative Function between Distant Sites in Bacterial Reaction Centers*

E. Alexov, M. Schiffer, P. Sebban, 2001, The Journal of Biological Chemistry.

omology-based modeling of 3 D structures of protein – protein complexes using lignments of modified sequence profiles etras

Emil Alexov, Petras J Kundrotas, Marc F Lensink, 2008 .

Predicting the Effect of Single Mutations on Protein Stability and Binding with Respect to Types of Mutations

Shailesh Kumar Panday, E. Alexov, P. Pandey, 2023, International Journal of Molecular Sciences.

Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity

Emil Alexov, Lin Li, Praveen Nedumpully-Govindan, 2014, Bioinform..

Predicting interacting and interfacial residues using continuous sequence segments.

Emil Alexov, Petras Kundrotas, E. Alexov, 2007, International journal of biological macromolecules.

Symmetrical electromagnetic waves in partially-filled plasma waveguide

E. Alexov, P. Malinov, S. Ivanov, 1989 .

Predicting 3D structures of transient protein-protein complexes by homology.

Emil Alexov, Petras J Kundrotas, E. Alexov, 2006, Biochimica et biophysica acta.

A missense mutation in CLIC2 associated with intellectual disability is predicted by in silico modeling to affect protein stability and dynamics

C. Schwartz, E. Alexov, Kyoko Takano, 2011, Proteins.

Anisotropic behavior of the pH dependence part of Young's modulus in a lysozyme triclinic crystal

B. Atanasov, E. Alexov, T. Ueki, 1995 .

On the pH‐optimum of activity and stability of proteins

E. Alexov, K. Talley, 2010, Proteins.

Molecular mechanisms of disease-causing missense mutations.

Shannon K. Stefl, A. Panchenko, E. Alexov, 2013, Journal of molecular biology.

Progress in developing Poisson-Boltzmann equation solvers

E. Alexov, M. Petukh, Lin Li, 2013, Molecular Based Mathematical Biology.

Chapter 2 – Structural and Energetic Basis of Molecular Recognition

B. Honig, E. Alexov, 2003 .

On the role of electrostatics in protein–protein interactions

Zhe Zhang, E. Alexov, Shawn Witham, 2011, Physical biology.

Mutations in the KDM5C ARID Domain and Their Plausible Association with Syndromic Claes-Jensen-Type Disease

Tugba G. Kucukkal, E. Alexov, Yunhui Peng, 2015, International journal of molecular sciences.

Research and applications: A rational free energy-based approach to understanding and targeting disease-causing missense mutations

Zhe Zhang, E. Alexov, M. Petukh, 2013, J. Am. Medical Informatics Assoc..

Modeling the electrostatic potential of asymmetric lipopolysaccharide membranes: The MEMPOT algorithm implemented in DelPhi

Roberta P. Dias, T. Soares, E. Alexov, 2014, J. Comput. Chem..

Understanding molecular effects of naturally occurring genetic differences.

Emil Alexov, E. Alexov, Michael Sternberg, 2013, Journal of molecular biology.