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1

Text mining for modeling of protein complexes enhanced by machine learning

Badal, Varsha D, Kundrotas, Petras J, Vakser, Ilya A, Elofsson, Arne

Journal:

Year:

2020

File:

PDF, 1.20 MB

2020

2

Modern Methods for Theoretical Physical Chemistry of Biopolymers || Monte Carlo method: some applications to problems in protein science

Kundrotas, Petras J.

Year:

2006

Language:

english

File:

PDF, 834 KB

english, 2006

3

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

4

Charge sequence coding in statistical modeling of unfolded proteins

Petras J. Kundrotas, Andrey Karshikoff

Journal:

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

Year:

2004

Language:

english

File:

PDF, 485 KB

english, 2004

5

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

6

Docking by structural similarity at protein-protein interfaces

Rohita Sinha, Petras J. Kundrotas, Ilya A. Vakser

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.14 MB

english, 2010

7

A Monte Carlo Sampling Scheme for the Ising Model

Roland Häggkvist, Anders Rosengren, Daniel Andrén, Petras Kundrotas, Per Håkan Lundow, Klas Markström

Journal:

Journal of Statistical Physics

Year:

2004

Language:

english

File:

PDF, 1.73 MB

english, 2004

8

Modeling of denatured state for calculation of the electrostatic contribution to protein stability

Petras J. Kundrotas, Andrey Karshikoff

Journal:

Protein Science

Year:

2002

Language:

english

File:

PDF, 86 KB

english, 2002

9

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

10

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

11

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

12

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

13

GWIDD: a comprehensive resource for genome-wide structural modeling of protein-protein interactions

Petras J Kundrotas, Zhengwei Zhu, Ilya A Vakser

Journal:

Year:

2012

Language:

english

File:

PDF, 448 KB

english, 2012

14

Electrostatic Properties of Protein-Protein Complexes

Kundrotas, Petras J., Alexov, Emil

Journal:

Biophysical Journal

Year:

2006

Language:

english

File:

PDF, 452 KB

english, 2006

15

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

16

Protein-protein alternative binding modes do not overlap

Kundrotas, Petras J., Vakser, Ilya A.

Journal:

Protein Science

Year:

2013

Language:

english

File:

PDF, 887 KB

english, 2013

17

Protein models: The Grand Challenge of protein docking

Anishchenko, Ivan, Kundrotas, Petras J., Tuzikov, Alexander V., Vakser, Ilya A.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 1.74 MB

english, 2014

18

Global and local structural similarity in protein-protein complexes: Implications for template-based docking

Kundrotas, Petras J., Vakser, Ilya A.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2013

Language:

english

File:

PDF, 940 KB

english, 2013

19

Structural templates for modeling homodimers

Kundrotas, Petras J., Vakser, Ilya A., Janin, Joël

Journal:

Protein Science

Year:

2013

Language:

english

File:

PDF, 1.14 MB

english, 2013

20

Template-Based Modeling of Protein-Protein Interfaces

Kundrotas, Petras, Vakser, Ilya A.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 39 KB

english, 2009

21

Docking Benchmark Set of Protein Models

Kundrotas, Petras J., Anishchenko, Ivan, Tuzikov, Alexander V., Vakser, Ilya A.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 33 KB

english, 2011

22

Docking by Structural Similarity at Protein-Protein Interfaces

Kundrotas, Petras, Sinha, Rohita, Vakser, Ilya A.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 37 KB

english, 2010

23

Structural Similarity in Modeling of Homodimers

Kundrotas, Petras, Vakser, Ilya, Janin, Joël

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 41 KB

english, 2014

24

Docking Benchmark Set of Protein Models

Anishchanka, Ivan, Kundrotas, Petras J., Tuzikov, Alexander V., Vakser, Ilya A.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 41 KB

english, 2014

25

Statistical Studies of Flexible Nonhomogeneous Polypeptide Chains

Kundrotas, Petras J.

Journal:

Biomacromolecules

Year:

2005

Language:

english

File:

PDF, 588 KB

english, 2005

26

Effects of charge–charge interactions on dimensions of unfolded proteins: A Monte Carlo study

Kundrotas, Petras J., Karshikoff, Andrey

Journal:

The Journal of Chemical Physics

Year:

2003

Language:

english

File:

PDF, 393 KB

english, 2003

27

Computation of the Ising partition function for two-dimensional square grids

Häggkvist, Roland, Rosengren, Anders, Andrén, Daniel, Kundrotas, Petras, Lundow, Per Håkan, Markström, Klas

Journal:

Physical Review E

Year:

2004

Language:

english

File:

PDF, 932 KB

english, 2004

28

Structural templates for comparative protein docking

Anishchenko, Ivan, Kundrotas, Petras J., Tuzikov, Alexander V., Vakser, Ilya A.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2015

Language:

english

File:

PDF, 1.98 MB

english, 2015

29

Protein models docking benchmark 2

Anishchenko, Ivan, Kundrotas, Petras J., Tuzikov, Alexander V., Vakser, Ilya A.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2015

Language:

english

File:

PDF, 1.53 MB

english, 2015

30

ASSESSING THE QUALITY OF THE HOMOLOGY-MODELED 3D STRUCTURES FROM ELECTROSTATIC STANDPOINT: TEST ON BACTERIAL NUCLEOSIDE MONOPHOSPHATE KINASE FAMILIES

KUNDROTAS, PETRAS, GEORGIEVA, PAULINA, SHOSHEVA, ALEXANDRA, CHRISTOVA, PETYA, ALEXOV, EMIL

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2007

Language:

english

File:

PDF, 623 KB

english, 2007

31

Accuracy of Protein-Protein Binding Sites in High-Throughput Template-Based Modeling

Kundrotas, Petras J., Vakser, Ilya A., Nussinov, Ruth

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 363 KB

english, 2010

32

Simulated unbound structures for benchmarking of protein docking in the Dockground resource

Kirys, Tatsiana, Ruvinsky, Anatoly M., Singla, Deepak, Tuzikov, Alexander V., Kundrotas, Petras J., Vakser, Ilya A.

Journal:

BMC Bioinformatics

Year:

2015

Language:

english

File:

PDF, 1.93 MB

english, 2015

33

Modeling Complexes of Modeled Proteins

Anishchenko, Ivan, Kundrotas, Petras J., Vakser, Ilya A.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2016

Language:

english

File:

PDF, 1.66 MB

english, 2016

34

Structural quality of unrefined models in protein docking

Anishchenko, Ivan, Kundrotas, Petras J., Vakser, Ilya A.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2016

Language:

english

File:

PDF, 1.17 MB

english, 2016

35

Refinement of Protein Docking with Atom-Atom Contact Potentials, Backbone Flexibility and Side-Chain Repacking

Dauzhenka, Taras, Anishchenko, Ivan, Kundrotas, Petras J., Vakser, Ilya A.

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 43 KB

english, 2017

36

Dockground : A comprehensive data resource for modeling of protein complexes

Kundrotas, Petras J., Anishchenko, Ivan, Dauzhenka, Taras, Kotthoff, Ian, Mnevets, Daniil, Copeland, Matthew M., Vakser, Ilya A.

Journal:

Protein Science

Year:

2017

Language:

english

File:

PDF, 1.59 MB

english, 2017

37

Modeling CAPRI targets 110-120 by template-based and free docking using contact potential and combined scoring function

Kundrotas, Petras J., Anishchenko, Ivan, Badal, Varsha D., Das, Madhurima, Dauzhenka, Taras, Vakser, Ilya A.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2017

Language:

english

File:

PDF, 1.26 MB

english, 2017

38

Structure-Function Relationships in Protein Complexes

Kundrotas, Petras, Belkin, Saveliy, Vakser, Ilya

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 40 KB

english, 2018

39

Natural language processing in text mining for structural modeling of protein complexes

Badal, Varsha D., Kundrotas, Petras J., Vakser, Ilya A.

Journal:

BMC Bioinformatics

Year:

2018

Language:

english

File:

PDF, 1.26 MB

english, 2018

40

Protein Docking by the Interface Structure Similarity: How Much Structure Is Needed?

Sinha, Rohita, Kundrotas, Petras J., Vakser, Ilya A., Keskin, Ozlem

Journal:

Year:

2012

Language:

english

File:

PDF, 229 KB

english, 2012

41

Inhibition of protein interactions: co-crystalized protein–protein interfaces are nearly as good as holo proteins in rigid-body ligand docking

Belkin, Saveliy, Kundrotas, Petras J., Vakser, Ilya A.

Journal:

Journal of Computer-Aided Molecular Design

Year:

2018

Language:

english

File:

PDF, 1.97 MB

english, 2018

42

Relative Contribution of the Refinement Steps to the Protein-Protein Docking Success Rate

Dauzhenka, Taras, Anishchenko, Ivan, Kundrotas, Petras J., Vakser, Ilya A.

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 40 KB

english, 2018

43

Contact Potential for Structure Prediction of Proteins and Protein Complexes from Potts Model

Anishchenko, Ivan, Kundrotas, Petras J., Vakser, Ilya A.

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 1.94 MB

english, 2018

44

Computational Feasibility of an Exhaustive Search of Side-Chain Conformations in Protein-Protein Docking

Dauzhenka, Taras, Kundrotas, Petras J., Vakser, Ilya A.

Journal:

Journal of Computational Chemistry

Year:

2018

Language:

english

File:

PDF, 2.46 MB

english, 2018

45

Gene ontology improves template selection in comparative protein docking

Hadarovich, Anna, Anishchenko, Ivan, Tuzikov, Alexander V., Kundrotas, Petras J., Vakser, Ilya A.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2018

Language:

english

File:

PDF, 2.30 MB

english, 2018

46

Modern Methods for Theoretical Physical Chemistry of Biopolymers || Monte Carlo method: some applications to problems in protein science

Kundrotas, Petras J.

Year:

2006

File:

PDF, 834 KB

2006

47

Application of Docking to Protein Models

Singh, Amar, Dauzhenka, Taras, Kundrotas, Petras, Sternberg, Michael J.E., Vakser, Ilya

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 43 KB

2020

48

Application of docking methodologies to modeled proteins

Singh, Amar, Dauzhenka, Taras, Kundrotas, Petras J., Sternberg, Michael J.E., Vakser, Ilya A.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2020

Language:

english

File:

PDF, 5.17 MB

english, 2020

49

How to choose templates for modeling of protein complexes: Insights from benchmarking templateâbased docking

Chakravarty, Devlina, McElfresh, GW, Kundrotas, Petras J., Vakser, Ilya A.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2020

File:

PDF, 2.78 MB

2020

50

Protein Docking Refinement with Systematic Conformational Search - Application to Models Inside the Docking Funnel

Dauzhenka, Taras, Anishchenko, Ivan, Kundrotas, Petras, Vakser, Ilya

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 50 KB

2020

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