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1

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

Tajielyato, Nayere, Li, Lin, Peng, Yunhui, Alper, Joshua, Alexov, Emil

Journal:

Scientific Reports

Year:

2018

Language:

english

File:

PDF, 2.51 MB

english, 2018

2

On the pH-optimum of activity and stability of proteins

Kemper Talley, Emil Alexov

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 265 KB

english, 2010

3

Protonation and pK changes in protein–ligand binding

Onufriev, Alexey V., Alexov, Emil

Journal:

Quarterly Reviews of Biophysics

Year:

2013

Language:

english

File:

PDF, 539 KB

english, 2013

4

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

Chakravorty, Arghya, Jia, Zhe, Li, Lin, Zhao, Shan, Alexov, Emil

Journal:

Journal of Chemical Theory and Computation

Year:

2018

Language:

english

File:

PDF, 3.57 MB

english, 2018

5

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

Tajielyato, Nayere, Alexov, Emil

Journal:

International Journal of Molecular Sciences

Year:

2019

File:

PDF, 7.77 MB

2019

6

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

Koirala, Mahesh, Alexov, Emil

Journal:

Journal of Theoretical and Computational Chemistry

Year:

2019

Language:

english

File:

PDF, 786 KB

english, 2019

7

Computational analysis of missense mutations causing Snyder-Robinson syndrome

Zhe Zhang, Shaolei Teng, Liangjiang Wang, Charles E. Schwartz, Emil Alexov

Journal:

Year:

2010

Language:

english

File:

PDF, 208 KB

english, 2010

8

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

Walter Rocchia, Sundaram Sridharan, Anthony Nicholls, Emil Alexov, Alessandro Chiabrera, Barry Honig

Journal:

Journal of Computational Chemistry

Year:

2002

Language:

english

File:

PDF, 210 KB

english, 2002

9

Predicting 3D structures of transient protein–protein complexes by homology

Petras J. Kundrotas, Emil Alexov

Journal:

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

Year:

2006

Language:

english

File:

PDF, 886 KB

english, 2006

10

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

Journal:

Year:

2004

Language:

english

File:

PDF, 560 KB

english, 2004

11

On the electrostatic component of protein-protein binding free energy

Kemper Talley, Carmen Ng, Michael Shoppell, Petras Kundrotas, Emil Alexov

Journal:

Year:

2008

Language:

english

File:

PDF, 1.26 MB

english, 2008

12

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

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 421 KB

english, 2003

13

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

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 858 KB

english, 2004

14

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

Rooplekha C. Mitra, Zhe Zhang, Emil Alexov

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2011

Language:

english

File:

PDF, 459 KB

english, 2011

15

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

Shawn Witham, Kyoko Takano, Charles Schwartz, Emil Alexov

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2011

Language:

english

File:

PDF, 431 KB

english, 2011

16

Developing hybrid approaches to predict pKa values of ionizable groups

Shawn Witham, Kemper Talley, Lin Wang, Zhe Zhang, Subhra Sarkar, Daquan Gao, Wei Yang, Emil Alexov

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2011

Language:

english

File:

PDF, 599 KB

english, 2011

17

Progress in the prediction of pKa values in proteins

Emil Alexov, Ernest L. Mehler, Nathan Baker, António M. Baptista, Yong Huang, Francesca Milletti, Jens Erik Nielsen, Damien Farrell, Tommy Carstensen, Mats H. M. Olsson, Jana K. Shen, Jim Warwicker, S

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2011

Language:

english

File:

PDF, 203 KB

english, 2011

18

The importance of the protein in controlling the electrochemistry of heme metalloproteins: methods of calculation and analysis

M. R. Gunner, Emil Alexov, Eduardo Torres, Samir Lipovaca

Journal:

JBIC Journal of Biological Inorganic Chemistry

Year:

1997

Language:

english

File:

PDF, 296 KB

english, 1997

19

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

Augustin Ofiteru, Nadia Bucurenci, Emil Alexov, Thomas Bertrand, Pierre Briozzo, Hélène Munier-Lehmann, Anne-Marie Gilles

Journal:

Year:

2007

Language:

english

File:

PDF, 899 KB

english, 2007

20

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

Chuan Li, Lin Li, Jie Zhang, Emil Alexov

Journal:

Journal of Computational Chemistry

Year:

2012

Language:

english

File:

PDF, 1.31 MB

english, 2012

21

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

Petras J Kundrotas, Emil G Alexov

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 459 KB

english, 2006

22

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

Petras Kundrotas, Paulina Georgieva, Alexandra Shosheva, Petya Christova, Emil Alexov

Journal:

International Journal of Biological Macromolecules

Year:

2007

Language:

english

File:

PDF, 1.51 MB

english, 2007

23

Predicting interacting and interfacial residues using continuous sequence segments

Petras Kundrotas, Emil Alexov

Journal:

International Journal of Biological Macromolecules

Year:

2007

Language:

english

File:

PDF, 728 KB

english, 2007

24

Homology-based modeling of 3D structures of protein–protein complexes using alignments of modified sequence profiles

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

Journal:

International Journal of Biological Macromolecules

Year:

2008

Language:

english

File:

PDF, 1.25 MB

english, 2008

25

On the Role of Structural Information in Remote Homology Detection and Sequence Alignment: New Methods Using Hybrid Sequence Profiles

Christopher L. Tang, Lei Xie, Ingrid Y.Y. Koh, Shoshana Posy, Emil Alexov, Barry Honig

Journal:

Journal of Molecular Biology

Year:

2003

Language:

english

File:

PDF, 1.60 MB

english, 2003

26

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

Michael J. Grey, Yuefeng Tang, Emil Alexov, C. James McKnight, Daniel P. Raleigh, Arthur G. Palmer III

Journal:

Journal of Molecular Biology

Year:

2006

Language:

english

File:

PDF, 463 KB

english, 2006

27

Calculation of pKas in RNA: On the Structural Origins and Functional Roles of Protonated Nucleotides

Christopher L. Tang, Emil Alexov, Anna Marie Pyle, Barry Honig

Journal:

Journal of Molecular Biology

Year:

2007

Language:

english

File:

PDF, 2.14 MB

english, 2007

28

Coating Single-Walled Carbon Nanotubes with Phospholipids

Wu, Yonnie, Hudson, JoAn S., Lu, Qi, Moore, Jessica M., Mount, Andrew S., Rao, Apparao M., Alexov, Emil, Ke, Pu Chun

Journal:

Journal of Physical Chemistry B

Year:

2006

Language:

english

File:

PDF, 195 KB

english, 2006

29

Predicting Nonspecific Ion Binding Using DelPhi

Petukh, Marharyta, Zhenirovskyy, Maxim, Li, Chuan, Li, Lin, Wang, Lin, Alexov, Emil

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 622 KB

english, 2012

30

Combining Conformational Flexibility and Continuum Electrostatics for Calculating pKas in Proteins

Georgescu, Roxana E., Alexov, Emil G., Gunner, Marilyn R.

Journal:

Biophysical Journal

Year:

2002

Language:

english

File:

PDF, 345 KB

english, 2002

31

Modeling Effects of Human Single Nucleotide Polymorphisms on Protein-Protein Interactions

Teng, Shaolei, Madej, Thomas, Panchenko, Anna, Alexov, Emil

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 499 KB

english, 2009

32

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

Smith, Nicholas, Campbell, Brandon, Li, Lin, Li, Chuan, Alexov, Emil

Journal:

BMC Structural Biology

Year:

2012

Language:

english

File:

PDF, 1.39 MB

english, 2012

33

DelPhi: a comprehensive suite for DelPhi software and associated resources

Li, Lin, Li, Chuan, Sarkar, Subhra, Zhang, Jie, Witham, Shawn, Zhang, Zhe, Wang, Lin, Smith, Nicholas, Petukh, Marharyta, Alexov, Emil

Journal:

Year:

2012

Language:

english

File:

PDF, 1.07 MB

english, 2012

34

Electrostatic Properties of Protein-Protein Complexes

Kundrotas, Petras J., Alexov, Emil

Journal:

Biophysical Journal

Year:

2006

Language:

english

File:

PDF, 452 KB

english, 2006

35

Poisson-Boltzmann Calculations of Nonspecific Salt Effects on Protein-Protein Binding Free Energies

Bertonati, Claudia, Honig, Barry, Alexov, Emil

Journal:

Biophysical Journal

Year:

2007

Language:

english

File:

PDF, 137 KB

english, 2007

36

Optimization of Electrostatic Interactions in Protein-Protein Complexes

Brock, Kelly, Talley, Kemper, Coley, Kacey, Kundrotas, Petras, Alexov, Emil

Journal:

Biophysical Journal

Year:

2007

Language:

english

File:

PDF, 194 KB

english, 2007

37

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

Li, Chuan, Petukh, Marharyta, Li, Lin, Alexov, Emil

Journal:

Journal of Computational Chemistry

Year:

2013

Language:

english

File:

PDF, 1.05 MB

english, 2013

38

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

Li, Lin, Li, Chuan, Zhang, Zhe, Alexov, Emil

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 4.56 MB

english, 2013

39

Comparative Study of Generalized Born Models: Born Radii and Peptide Folding

Zhu, Jiang, Alexov, Emil, Honig, Barry

Journal:

Journal of Physical Chemistry B

Year:

2005

Language:

english

File:

PDF, 661 KB

english, 2005

40

Molecular Mechanisms of Disease-Causing Missense Mutations

Stefl, Shannon, Nishi, Hafumi, Petukh, Marharyta, Panchenko, Anna R., Alexov, Emil

Journal:

Journal of Molecular Biology

Year:

2013

Language:

english

File:

PDF, 999 KB

english, 2013

41

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

Dias, Roberta P., Li, Lin, Soares, Thereza A., Alexov, Emil

Journal:

Journal of Computational Chemistry

Year:

2014

Language:

english

File:

PDF, 1.21 MB

english, 2014

42

Enhancing Human Spermine Synthase Activity by Site Directed Mutations

Zhang, Zhe, Pegg, Anthony, Ikeguchi, Yoshihiko, Alexov, Emil

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 38 KB

english, 2013

43

NEW ZEALAND.

Zhang, Zhe, Pegg, Anthony, Ikeguchi, Yoshihiko, Alexov, Emil

Journal:

Year:

1893

Language:

english

File:

PDF, 400 KB

english, 1893

44

Golgi studies of the neurons in layer II of the dorsal horn of the medulla (trigeminal nucleus caudalis)

Zhang, Zhe, Pegg, Anthony, Ikeguchi, Yoshihiko, Alexov, Emil

Journal:

Year:

1979

Language:

english

File:

PDF, 167 KB

english, 1979

45

In Silico Investigation of the Molecular Effects Caused by Missense Mutations in Spermine Sythase Gene Associated with Human Mental Retardation

Zhe, Zhang, Shaolei, Teng, Alexov, Emil

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 49 KB

english, 2010

46

Modeling Proteins and Small Molecules with Inhomogeneous Dielectric Function: Implementation in Delphi

Li, Lin, Li, Chuan, Alexov, Emil

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 34 KB

english, 2013

47

Multi-Level and Interleaved Poisson-Boltzmann (MLIPB) Method for Parallel Computing of the Electrostatics and its Application in Delphi

Li, Chuan, Petukh, Marharyta, Li, Lin, Alexov, Emil

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 35 KB

english, 2013

48

New Parallelized DelPhi: Fast and Efficient Poisson-Boltzmann Solver to Calculate Electrostatics of Large Supramolecular Structures

Li, Chuan, Zhenirovskyy, Maxim, Li, Lin, Alexov, Emil

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 41 KB

english, 2012

49

Modeling CLIC2-RyR Interactions and the Effect of Disease Causing Mutation

Witham, Shawn, Alexov, Emil

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 36 KB

english, 2012

50

In Silico Investigation of a Missense Mutation in CLIC2 Associated with Intellectual Disability

Witham, Shawn, Takano, Kyoko, Schwartz, Charles, Alexov, Emil

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 51 KB

english, 2011

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