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1

Modeling the Impact of Seasonal Weather Variations on the Infectiology of Brucellosis

Nyerere, Nkuba, Luboobi, Livingstone S., Mpeshe, Saul C., Shirima, Gabriel M., Kloczkowski, Andrzej

Journal:

Computational and Mathematical Methods in Medicine

Year:

2020

File:

PDF, 1.26 MB

2020

2

Loop Folds in Proteins and Evolutionary Conservation of Folding Nuclei

Kloczkowski, Andrzej, Jernigan, Robert L.

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2002

Language:

english

File:

PDF, 239 KB

english, 2002

3

Main-Chain Lyotropic Liquid-Crystalline Elastomers. 1. Syntheses of Cross-Linked Polyisocyanate Gels Acquiring Liquid-Crystalline Behavior in the Swollen State

Zhao, Wenyan, Kloczkowski, Andrzej, Mark, James E., Erman, Burak, Bahar, Ivet

Journal:

Year:

1996

Language:

english

File:

PDF, 568 KB

english, 1996

4

Main-Chain Lyotropic Liquid-Crystalline Elastomers. 2. Orientation and Mechanical Properties of Polyisocyanate Films

Zhao, Wenyan, Kloczkowski, Andrzej, Mark, James E., Erman, Burak, Bahar, Ivet

Journal:

Year:

1996

Language:

english

File:

PDF, 543 KB

english, 1996

5

A simple derivation of the exponent γ for Gaussian chains with excluded volume

Andrzej Kloczkowski, James E. Mark, Burak Erman

Journal:

Macromolecular Theory and Simulations

Year:

1995

Language:

english

File:

PDF, 286 KB

english, 1995

6

Small-Angle Neutron Scattering from Elastomeric Networks in which the Junctions Alternate Regularly in their Functionality

Aris Skliros, James E. Mark, Andrzej Kloczkowski

Journal:

Macromolecular Theory and Simulations

Year:

2009

Language:

english

File:

PDF, 429 KB

english, 2009

7

Filler-induced deformations of amorphous polyethylene chains. The effects of the deformations on elastomeric properties, and some comparisons with experiments

Mohammed A. Sharaf, Andrzej Kloczkowski, Taner Z. Sen, Karl I. Jacob, James E. Mark

Journal:

European Polymer Journal

Year:

2006

Language:

english

File:

PDF, 228 KB

english, 2006

8

The transfer matrix method for lattice proteins—an application with cooperative interactions

Andrzej Kloczkowski, Taner Z. Sen, Robert L. Jernigan

Journal:

Year:

2004

Language:

english

File:

PDF, 317 KB

english, 2004

9

Protein Conformational Computations-special issue of Polymer

Andrzej Kloczkowski, Robert L. Jernigan

Journal:

Year:

2004

Language:

english

File:

PDF, 55 KB

english, 2004

10

The largest eigenvalue method for stereo-regular vinyl chains

Andrzej Kloczkowski, Taner Z. Sen, Mohammed A. Sharaf

Journal:

Year:

2005

Language:

english

File:

PDF, 209 KB

english, 2005

11

Modeling the elastomeric properties of stereoregular polypropylenes in nanocomposites with spherical fillers

Taner Z. Sen, Mohammed A. Sharaf, James E. Mark, Andrzej Kloczkowski

Journal:

Year:

2005

Language:

english

File:

PDF, 194 KB

english, 2005

12

Some simulations on filler reinforcement in elastomers

James E. Mark, Reda Abou-Hussein, Taner Z. Sen, Andrzej Kloczkowski

Journal:

Year:

2005

Language:

english

File:

PDF, 335 KB

english, 2005

13

MAVENs: Motion analysis and visualization of elastic networks and structural ensembles

Michael T Zimmermann, Andrzej Kloczkowski, Robert L Jernigan

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 1.38 MB

english, 2011

14

Structural interpretation of protein-protein interaction network

Ataur R Katebi, Andrzej Kloczkowski, Robert L Jernigan

Journal:

BMC Structural Biology

Year:

2010

Language:

english

File:

PDF, 7.08 MB

english, 2010

15

The origin and extent of coarse-grained regularities in protein internal packing

Zerrin Bagci, Andrzej Kloczkowski, Robert L. Jernigan, Ivet Bahar

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 574 KB

english, 2003

16

Inferring ideal amino acid interaction forms from statistical protein contact potentials

Piotr Pokarowski, Andrzej Kloczkowski, Robert L. Jernigan, Neha S. Kothari, Maria Pokarowska, Andrzej Kolinski

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 1.12 MB

english, 2005

17

Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys

Yaping Feng, Andrzej Kloczkowski, Robert L. Jernigan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2007

Language:

english

File:

PDF, 311 KB

english, 2007

18

Ideal amino acid exchange forms for approximating substitution matrices

Piotr Pokarowski, Andrzej Kloczkowski, Szymon Nowakowski, Maria Pokarowska, Robert L. Jernigan, Andrzej Kolinski

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2007

Language:

english

File:

PDF, 4.52 MB

english, 2007

19

Predicting the order in which contacts are broken during single molecule protein stretching experiments

Joanna I. Sułkowska, Andrzej Kloczkowski, Taner Z. Sen, Marek Cieplak, Robert L. Jernigan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.07 MB

english, 2008

20

Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron

Yaping Feng, Robert L. Jernigan, Andrzej Kloczkowski

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 297 KB

english, 2008

21

The energy profiles of atomic conformational transition intermediates of adenylate kinase

Yaping Feng, Lei Yang, Andrzej Kloczkowski, Robert L. Jernigan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2009

Language:

english

File:

PDF, 274 KB

english, 2009

22

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

23

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

24

Molecular modeling of matrix chain deformation in nanofiber filled composites

Mohammed A. Sharaf, Andrzej Kloczkowski, Taner Z. Sen, Karl I. Jacob, James E. Mark

Journal:

Colloid & Polymer Science

Year:

2006

Language:

english

File:

PDF, 221 KB

english, 2006

25

Support-vector-machine classification of linear functional motifs in proteins

Dariusz Plewczynski, Adrian Tkacz, Lucjan Stanisław Wyrwicz, Adam Godzik, Andrzej Kloczkowski, Leszek Rychlewski

Journal:

Journal of Molecular Modeling

Year:

2006

Language:

english

File:

PDF, 175 KB

english, 2006

26

Molecular modeling of phosphorylation sites in proteins using a database of local structure segments

Dariusz Plewczynski, Lukasz Jaroszewski, Adam Godzik, Andrzej Kloczkowski, Leszek Rychlewski

Journal:

Journal of Molecular Modeling

Year:

2005

Language:

english

File:

PDF, 385 KB

english, 2005

27

Distance matrix-based approach to protein structure prediction

Andrzej Kloczkowski, Robert L. Jernigan, Zhijun Wu, Guang Song, Lei Yang, Andrzej Kolinski, Piotr Pokarowski

Journal:

Journal of Structural and Functional Genomics

Year:

2009

Language:

english

File:

PDF, 667 KB

english, 2009

28

Statistical measures on residue-level protein structural properties

Yuanyuan Huang, Stephen Bonett, Andrzej Kloczkowski, Robert Jernigan, Zhijun Wu

Journal:

Journal of Structural and Functional Genomics

Year:

2011

Language:

english

File:

PDF, 1.16 MB

english, 2011

29

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

30

Prediction of protein secondary structure by mining structural fragment database

Haitao Cheng, Taner Z. Sen, Andrzej Kloczkowski, Dimitris Margaritis, Robert L. Jernigan

Journal:

Year:

2005

Language:

english

File:

PDF, 218 KB

english, 2005

31

A Consensus Data Mining secondary structure prediction by combining GOR V and Fragment Database Mining

Taner Z. Sen, Haitao Cheng, Andrzej Kloczkowski, Robert L. Jernigan

Journal:

Protein Science

Year:

2006

Language:

english

File:

PDF, 344 KB

english, 2006

32

A DNA-Centric Look at Protein-DNA Complexes

Taner Z. Sen, Andrzej Kloczkowski, Robert L. Jernigan

Journal:

Year:

2006

Language:

english

File:

PDF, 45 KB

english, 2006

33

Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials

Yaping Feng, Andrzej Kloczkowski, Robert L Jernigan

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 299 KB

english, 2010

34

Predicting binding sites of hydrolase-inhibitor complexes by combining several methods

Taner Z Sen, Andrzej Kloczkowski, Robert L Jernigan, Changhui Yan, Vasant Honavar, Kai-Ming Ho, Cai-Zhuang Wang, Yungok Ihm, Haibo Cao, Xun Gu, Drena Dobbs

Journal:

BMC Bioinformatics

Year:

2004

Language:

english

File:

PDF, 790 KB

english, 2004

35

Functional clustering of yeast proteins from the protein-protein interaction network

Taner Z Sen, Andrzej Kloczkowski, Robert L Jernigan

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 641 KB

english, 2006

36

Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable

Myron Peto, Andrzej Kloczkowski, Vasant Honavar, Robert L Jernigan

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 506 KB

english, 2008

37

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

38

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

39

Predicting the Complex Structure and Functional Motions of the Outer Membrane Transporter and Signal Transducer FecA

Sen, Taner Z., Kloster, Margaret, Jernigan, Robert L., Kolinski, Andrzej, Bujnicki, Janusz M., Kloczkowski, Andrzej

Journal:

Biophysical Journal

Year:

2008

Language:

english

File:

PDF, 1.35 MB

english, 2008

40

Novel High-Performance Materials from Starch. 2. Orientation and Mechanical Properties of Lightly Cross-Linked Starch−Ether Films

Zhao, Wenyan, Kloczkowski, Andrzej, Mark, James E., Erman, Burak

Journal:

Chemistry of Materials

Year:

1998

Language:

english

File:

PDF, 178 KB

english, 1998

41

The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models

Sen, Taner Z., Feng, Yaping, Garcia, John V., Kloczkowski, Andrzej, Jernigan, Robert L.

Journal:

Journal of Chemical Theory and Computation

Year:

2006

Language:

english

File:

PDF, 433 KB

english, 2006

42

A Diffused-Constraint Theory for the Elasticity of Amorphous Polymer Networks. 1. Fundamentals and Stress-Strain Isotherms in Elongation

Kloczkowski, Andrzej, Mark, James E., Erman, Burak

Journal:

Year:

1995

Language:

english

File:

PDF, 814 KB

english, 1995

43

Book Review of Molecular Modeling of Proteins. Methods in Molecular Biology, 443 Molecular Modeling of Proteins. Methods in Molecular Biology, 443 . Edited by Andreas Kukol (University of Hertfordshire, U.K.). Humana Press : Totowa . 2008. xii + 390 pp. $99.50. ISBN 978-1-58829-864-5 .

Kloczkowski, Andrzej, Jernigan, Robert L.

Journal:

Journal of the American Chemical Society

Year:

2008

Language:

english

File:

PDF, 71 KB

english, 2008

44

A global machine learning based scoring function for protein structure prediction

Faraggi, Eshel, Kloczkowski, Andrzej

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 125 KB

english, 2014

45

[IEEE 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshop, BIBMW - Washington, DC, USA (2009.11.1-2009.11.4)] 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshop - Computational testing of protein-protein interactions

Katebi, Ataur R., Kloczkowski, Andrzej, Jeringan, Robert L.

Year:

2009

Language:

english

File:

PDF, 461 KB

english, 2009

46

Multi-Body Knowledge-Based Potentials for Protein Structure Prediction Evaluation

Feng, Yaping, Jernigan, Robert L., Kloczkowski, Andrzej

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 33 KB

english, 2010

47

A Global Machine Learning Based Scoring Function for Protein Structure Prediction

Faraggi, Eshel, Kloczkowski, Andrzej

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 72 KB

english, 2014

48

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

49

MQAPmulti2 and MQAPsingle2:Toward the Estimation of Model Quality When Not Only Many Models are Available

Pawlowski, Marcin, Kloczkowski, Andrzej

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 36 KB

english, 2013

50

De Novo Protein Structure Determination from Incomplete Experimental Data

Gront, Dominik, Kloczkowski, Andrzej

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 37 KB

english, 2013