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1

[IEEE 2013 International Conference on Electromagnetics in Advanced Applications (ICEAA) - Torino (Turin), Italy (2013.09.9-2013.09.13)] 2013 International Conference on Electromagnetics in Advanced Applications (ICEAA) - Signal-power integrity and EMI analysis for singlechip and multi-chip-module applications

Wane, Sidina, Erdem, Aykut, Le Grontec, Alexis, Tesson, Olivier, Bardy, Serge, Kloczkowski, Robert, Abessolo, Dolphin, Mattheijssen, Paul

Year:

2013

Language:

english

File:

PDF, 1.42 MB

english, 2013

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

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

4

Protein Conformational Computations-special issue of Polymer

Andrzej Kloczkowski, Robert L. Jernigan

Journal:

Year:

2004

Language:

english

File:

PDF, 55 KB

english, 2004

5

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

6

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

7

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

8

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

9

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

10

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

11

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

12

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

13

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

14

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

15

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

16

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

17

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

18

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

19

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

20

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

21

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

22

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

23

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

24

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

25

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

26

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

27

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

28

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

29

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

30

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

31

[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

32

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

33

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

34

Effects of Protein Subunits Removal on the Computed Motions of Partial 30S Structures of the Ribosome

Yan, Aimin, Wang, Yongmei, Kloczkowski, Andrzej, Jernigan, Robert L.

Journal:

Journal of Chemical Theory and Computation

Year:

2008

Language:

english

File:

PDF, 1.54 MB

english, 2008

35

Prediction of Side Chain Orientations in Proteins by Statistical Machine Learning Methods

Yan, Aimin, Kloczkowski, Andrzej, Hofmann, Heike, Jernigan, Robert L.

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2007

Language:

english

File:

PDF, 1.29 MB

english, 2007

36

Combining Statistical Potentials with Dynamics-Based Entropies Improves Selection from Protein Decoys and Docking Poses

Zimmermann, Michael T., Leelananda, Sumudu P., Kloczkowski, Andrzej, Jernigan, Robert L.

Journal:

Journal of Physical Chemistry B

Year:

2012

Language:

english

File:

PDF, 332 KB

english, 2012

37

Models To Approximate the Motions of Protein Loops

Skliros, Aris, Jernigan, Robert L., Kloczkowski, Andrzej

Journal:

Journal of Chemical Theory and Computation

Year:

2010

Language:

english

File:

PDF, 1.49 MB

english, 2010

38

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

39

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

40

P.R.E.S.S. — AN R-PACKAGE FOR EXPLORING RESIDUAL-LEVEL PROTEIN STRUCTURAL STATISTICS

HUANG, YUANYUAN, BONETT, STEPHEN, KLOCZKOWSKI, ANDRZEJ, JERNIGAN, ROBERT, WU, ZHIJUN

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2012

Language:

english

File:

PDF, 636 KB

english, 2012

41

Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step

Kamil Steczkiewicz, Michael T. Zimmermann, Mateusz Kurcinski, Benjamin A. Lewis, Drena Dobbs, Andrzej Kloczkowski, Robert L. Jernigan, Andrzej Kolinski and Krzysztof Ginalski

Journal:

Proceedings of the National Academy of Sciences

Year:

2011

Language:

english

File:

PDF, 1.43 MB

english, 2011

42

The ribosome structure controls and directs mRNA entry, translocation and exit dynamics

Kurkcuoglu, Ozge, Doruker, Pemra, Sen, Taner Z, Kloczkowski, Andrzej, Jernigan, Robert L

Journal:

Physical Biology

Year:

2008

Language:

english

File:

PDF, 1.47 MB

english, 2008

43

The importance of slow motions for protein functional loops

Skliros, Aris, Zimmermann, Michael T, Chakraborty, Debkanta, Saraswathi, Saras, Katebi, Ataur R, Leelananda, Sumudu P, Kloczkowski, Andrzej, Jernigan, Robert L

Journal:

Physical Biology

Year:

2012

Language:

english

File:

PDF, 603 KB

english, 2012

44

[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 - Immunoglobulin functional motions and their effects on the complementarity determining regions

Zimmermann, Michael T., Skliros, Aris, Saraswathi, Saras, Kloczkowski, Andrzej, Jernigan, Robert L.

Year:

2010

Language:

english

File:

PDF, 861 KB

english, 2010

45

Generation and enumeration of compact conformations on the two-dimensional triangular and three-dimensional fcc lattices

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

Journal:

The Journal of Chemical Physics

Year:

2007

Language:

english

File:

PDF, 988 KB

english, 2007

46

[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

47

Exploration of the relationship between topology and designability of conformations

Leelananda, Sumudu P., Towfic, Fadi, Jernigan, Robert L., Kloczkowski, Andrzej

Journal:

The Journal of Chemical Physics

Year:

2011

Language:

english

File:

PDF, 472 KB

english, 2011

48

Shape-dependent designability studies of lattice proteins

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

Journal:

Journal of Physics Condensed Matter

Year:

2007

Language:

english

File:

PDF, 390 KB

english, 2007

49

Predicting Designability of Small Proteins from Graph Features of Contact Maps

Leelananda, Sumudu P., Jernigan, Robert L., Kloczkowski, Andrzej

Journal:

Journal of Computational Biology

Year:

2016

Language:

english

File:

PDF, 618 KB

english, 2016

50

Fold-specific sequence scoring improves protein sequence matching

Leelananda, Sumudu P., Kloczkowski, Andrzej, Jernigan, Robert L.

Journal:

BMC Bioinformatics

Year:

2016

Language:

english

File:

PDF, 1.03 MB

english, 2016