Emil Alexov to Proteins
This is a "connection" page, showing publications Emil Alexov has written about Proteins.
Connection Strength
13.343
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SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein-protein binding affinity. Bioinformatics. 2021 05 17; 37(7):992-999.
Score: 0.562
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SAAFEC-SEQ: A Sequence-Based Method for Predicting the Effect of Single Point Mutations on Protein Thermodynamic Stability. Int J Mol Sci. 2021 Jan 09; 22(2).
Score: 0.548
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BION-2: Predicting Positions of Non-Specifically Bound Ions on Protein Surface by a Gaussian-Based Treatment of Electrostatics. Int J Mol Sci. 2020 Dec 29; 22(1).
Score: 0.547
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SAAMBE-3D: Predicting Effect of Mutations on Protein-Protein Interactions. Int J Mol Sci. 2020 Apr 07; 21(7).
Score: 0.520
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Capturing the Effects of Explicit Waters in Implicit Electrostatics Modeling: Qualitative Justification of Gaussian-Based Dielectric Models in DelPhi. J Chem Inf Model. 2020 04 27; 60(4):2229-2246.
Score: 0.519
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PKAD: a database of experimentally measured pKa values of ionizable groups in proteins. Database (Oxford). 2019 01 01; 2019.
Score: 0.477
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DelPhiPKa: Including salt in the calculations and enabling polar residues to titrate. Proteins. 2018 12; 86(12):1277-1283.
Score: 0.471
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DelPhiForce web server: electrostatic forces and energy calculations and visualization. Bioinformatics. 2017 Nov 15; 33(22):3661-3663.
Score: 0.441
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A New DelPhi Feature for Modeling Electrostatic Potential around Proteins: Role of Bound Ions and Implications for Zeta-Potential. Langmuir. 2017 03 07; 33(9):2283-2295.
Score: 0.419
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DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding. J Comput Chem. 2017 04 05; 38(9):584-593.
Score: 0.417
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SAAMBE: Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations. Int J Mol Sci. 2016 Apr 12; 17(4):547.
Score: 0.395
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Investigating the linkage between disease-causing amino acid variants and their effect on protein stability and binding. Proteins. 2016 Feb; 84(2):232-9.
Score: 0.388
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DelPhiPKa web server: predicting pKa of proteins, RNAs and DNAs. Bioinformatics. 2016 Feb 15; 32(4):614-5.
Score: 0.382
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Statistical investigation of surface bound ions and further development of BION server to include pH and salt dependence. J Comput Chem. 2015 Dec 15; 36(32):2381-93.
Score: 0.382
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pKa predictions for proteins, RNAs, and DNAs with the Gaussian dielectric function using DelPhi pKa. Proteins. 2015 Dec; 83(12):2186-97.
Score: 0.381
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Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method. PLoS Comput Biol. 2015 Jul; 11(7):e1004276.
Score: 0.374
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Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins. Curr Opin Struct Biol. 2015 Jun; 32:18-24.
Score: 0.364
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Molecular mechanisms of disease-causing missense mutations. J Mol Biol. 2013 Nov 01; 425(21):3919-36.
Score: 0.326
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Protonation and pK changes in protein-ligand binding. Q Rev Biophys. 2013 May; 46(2):181-209.
Score: 0.322
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BION web server: predicting non-specifically bound surface ions. Bioinformatics. 2013 Mar 15; 29(6):805-6.
Score: 0.316
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Protein Nano-Object Integrator (ProNOI) for generating atomic style objects for molecular modeling. BMC Struct Biol. 2012 Dec 05; 12:31.
Score: 0.313
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Predicting nonspecific ion binding using DelPhi. Biophys J. 2012 Jun 20; 102(12):2885-93.
Score: 0.303
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Predicting folding free energy changes upon single point mutations. Bioinformatics. 2012 Mar 01; 28(5):664-71.
Score: 0.294
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Progress in the prediction of pKa values in proteins. Proteins. 2011 Dec; 79(12):3260-75.
Score: 0.289
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On the role of electrostatics in protein-protein interactions. Phys Biol. 2011 Jun; 8(3):035001.
Score: 0.281
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On the pH-optimum of activity and stability of proteins. Proteins. 2010 Sep; 78(12):2699-706.
Score: 0.267
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Modeling effects of human single nucleotide polymorphisms on protein-protein interactions. Biophys J. 2009 Mar 18; 96(6):2178-88.
Score: 0.242
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Protein-protein interactions. Curr Pharm Biotechnol. 2008 Apr; 9(2):55-6.
Score: 0.226
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Approaches and resources for prediction of the effects of non-synonymous single nucleotide polymorphism on protein function and interactions. Curr Pharm Biotechnol. 2008 Apr; 9(2):123-33.
Score: 0.226
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Optimization of electrostatic interactions in protein-protein complexes. Biophys J. 2007 Nov 15; 93(10):3340-52.
Score: 0.216
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Predicting interacting and interfacial residues using continuous sequence segments. Int J Biol Macromol. 2007 Dec 01; 41(5):615-23.
Score: 0.216
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Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies. Biophys J. 2007 Mar 15; 92(6):1891-9.
Score: 0.208
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Predicting 3D structures of transient protein-protein complexes by homology. Biochim Biophys Acta. 2006 Sep; 1764(9):1498-511.
Score: 0.202
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Electrostatic properties of protein-protein complexes. Biophys J. 2006 Sep 01; 91(5):1724-36.
Score: 0.200
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Numerical calculations of the pH of maximal protein stability. The effect of the sequence composition and three-dimensional structure. Eur J Biochem. 2004 Jan; 271(1):173-85.
Score: 0.169
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Role of the protein side-chain fluctuations on the strength of pair-wise electrostatic interactions: comparing experimental with computed pK(a)s. Proteins. 2003 Jan 01; 50(1):94-103.
Score: 0.157
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Electrostatics in Computational Biophysics and Its Implications for Disease Effects. Int J Mol Sci. 2022 Sep 07; 23(18).
Score: 0.154
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On regularization of charge singularities in solving the Poisson-Boltzmann equation with a smooth solute-solvent boundary. Math Biosci Eng. 2021 01 21; 18(2):1370-1405.
Score: 0.137
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A pragmatic approach to structure based calculation of coupled proton and electron transfer in proteins. Biochim Biophys Acta. 2000 May 12; 1458(1):63-87.
Score: 0.131
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A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states. J Math Biol. 2019 07; 79(2):631-672.
Score: 0.122
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Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases. Int J Mol Sci. 2019 Jan 28; 20(3).
Score: 0.120
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SAAFEC: Predicting the Effect of Single Point Mutations on Protein Folding Free Energy Using a Knowledge-Modified MM/PBSA Approach. Int J Mol Sci. 2016 Apr 07; 17(4):512.
Score: 0.099
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ProBLM web server: protein and membrane placement and orientation package. Comput Math Methods Med. 2014; 2014:838259.
Score: 0.087
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Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives. BMC Bioinformatics. 2006 Nov 16; 7:503.
Score: 0.051
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On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles. J Mol Biol. 2003 Dec 12; 334(5):1043-62.
Score: 0.042
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Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins. 2003; 53 Suppl 6:430-5.
Score: 0.039