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1

Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models

Pawel Gniewek, Sumudu P. Leelananda, Andrzej Kolinski, Robert L. Jernigan, Andrzej Kloczkowski

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2011

Language:

english

File:

PDF, 788 KB

english, 2011

2

How noise in force fields can affect the structural refinement of protein models?

Pawel Gniewek, Andrzej Kolinski, Robert L Jernigan, Andrzej Kloczkowski

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2012

Language:

english

File:

PDF, 290 KB

english, 2012

3

Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models

Michael T. Zimmermann, Sumudu P. Leelananda, Pawel Gniewek, Yaping Feng, Robert L. Jernigan, Andrzej Kloczkowski

Journal:

Journal of Structural and Functional Genomics

Year:

2011

Language:

english

File:

PDF, 471 KB

english, 2011

4

Protein Secondary Structure Prediction Using Knowledge-Based Potentials and An Ensemble of Classifiers

Sundararajan, Saraswathi, Gniewek, Pawel, Jernigan, Robert L., Kolinski, Andrzej, Kloczkowski, Andrzej

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 36 KB

english, 2010

5

Coarse-Grained Monte Carlo Simulations of Mucus: Structure, Dynamics, and Thermodynamics

Gniewek, Pawel, Kolinski, Andrzej

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 663 KB

english, 2010

6

ANM Normal Modes Show the Directions for Protein Structure Refinement

Gniewek, Pawel, Kolinski, Andrzej, Jernigan, Robert L., Kloczkowski, Andrzej

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 34 KB

english, 2012

7

Coarse-Grained Modeling of Mucus Barrier Properties

Gniewek, Pawel, Kolinski, Andrzej

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 872 KB

english, 2012

8

New Methods to Improve Protein Structure Prediction and Refinement

Kloczkowski, Andrzej, Gniewek, Pawel, Faraggi, Eshel, Zimmermann, Michael, Gront, Dominik, Pawlowski, Marcin, Jernigan, Robert L., Kolinski, Andrzej

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 36 KB

english, 2013

9

Optimization of Profile-to-Profile Alignment Parameters for One-Dimensional Threading

Gniewek, Pawel, Kolinski, Andrzej, Gront, Dominik

Journal:

Journal of Computational Biology

Year:

2012

Language:

english

File:

PDF, 262 KB

english, 2012

10

Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models

Pawel, Gniewek, Leelananda, Sumudu P., Andrzej, Kolinski, Jernigan, Robert L., Andrzej, Kloczkowski

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 32 KB

english, 2014

11

Elastic network normal modes provide a basis for protein structure refinement

Gniewek, Pawel, Kolinski, Andrzej, Jernigan, Robert L., Kloczkowski, Andrzej

Journal:

The Journal of Chemical Physics

Year:

2012

Language:

english

File:

PDF, 1.21 MB

english, 2012

12

BioShell-Threading: versatile Monte Carlo package for protein 3D threading

Gniewek, Pawel, Kolinski, Andrzej, Kloczkowski, Andrzej, Gront, Dominik

Journal:

BMC Bioinformatics

Year:

2014

Language:

english

File:

PDF, 2.01 MB

english, 2014

13

Note: A simple picture of subdiffusive polymer motion from stochastic simulations

Gniewek, Pawel, Kolinski, Andrzej

Journal:

The Journal of Chemical Physics

Year:

2011

Language:

english

File:

PDF, 111 KB

english, 2011

14

[ACM Press the First ACM International Conference - Niagara Falls, New York (2010.08.02-2010.08.04)] Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology - BCB '10 - Immunological implications of a structural analysis of two different porcine IL1β proteins expressed in macrophages and embryos

Katebi, Ataur R., Gniewek, Pawel, Zimmermann, Michael, Saraswathi, Saras, Gong, Zhenming, Tuggle, Christopher K., Kloczkowski, Andrzej, Jernigan, Robert L.

Year:

2010

Language:

english

File:

PDF, 674 KB

english, 2010

15

Self-driven jamming in growing microbial populations

Delarue, Morgan, Hartung, Jörn, Schreck, Carl, Gniewek, Pawel, Hu, Lucy, Herminghaus, Stephan, Hallatschek, Oskar

Journal:

Year:

2016

Language:

english

File:

PDF, 1.25 MB

english, 2016

16

Fluid flow through packings of elastic shells

Gniewek, Pawel, Hallatschek, Oskar

Journal:

Physical Review E

Year:

2019

File:

PDF, 2.76 MB

2019

17

Fluid flow through packings of elastic shells

Gniewek, Pawel, Hallatschek, Oskar

Journal:

Physical Review E

Year:

2019

Language:

english

File:

PDF, 2.76 MB

english, 2019

18

Biomechanical Feedback Strengthens Jammed Cellular Packings

Gniewek, Pawel, Schreck, Carl F., Hallatschek, Oskar

Journal:

Physical Review Letters

Year:

2019

Language:

english

File:

PDF, 1.25 MB

english, 2019