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1

KnotProt 2.0: a database of proteins with knots and other entangled structures

Dabrowski-Tumanski, Pawel, Rubach, Pawel, Goundaroulis, Dimos, Dorier, Julien, Sułkowski, Piotr, Millett, Kenneth C, Rawdon, Eric J, Stasiak, Andrzej, Sulkowska, Joanna I

Journal:

Nucleic Acids Research

Year:

2018

Language:

english

File:

PDF, 2.54 MB

english, 2018

2

Knotting pathways in proteins

Sułkowska, Joanna I., Noel, Jeffrey K., Ramírez‑Sarmiento, César A., Rawdon, Eric J., Millett, Kenneth C., Onuchic, José N.

Journal:

Biochemical Society Transactions

Year:

2013

Language:

english

File:

PDF, 354 KB

english, 2013

3

Möbius energy of thick knots

Eric J. Rawdon, Jonathan Simon

Journal:

Topology and its Applications

Year:

2002

Language:

english

File:

PDF, 111 KB

english, 2002

4

Length of the tightest trefoil knot

Baranska, Justyna, Pieranski, Piotr, Przybyl, Sylwester, Rawdon, Eric J.

Journal:

Physical Review E

Year:

2004

Language:

english

File:

PDF, 606 KB

english, 2004

5

[Series on Knots and Everything] Physical and Numerical Models in Knot Theory Volume 36 (Including Applications to the Life Sciences) || PROTEIN FOLDS, KNOTS AND TANGLES

Calvo, Jorge A, Millett, Kenneth C, Rawdon, Eric J, Stasiak, Andrzej

Year:

2005

Language:

english

File:

PDF, 1.65 MB

english, 2005

6

Cumulative Shapes of Knotted Polymers

Rawdon, Eric J., Millett, Kenneth C., Tran, Vy T., Stasiak, Andrzej

Journal:

Progress of Theoretical Physics Supplement

Year:

2011

Language:

english

File:

PDF, 2.69 MB

english, 2011

7

Total curvature and total torsion of knotted random polygons in confinement

Diao, Yuanan, Ernst, Claus, Rawdon, Eric, Ziegler, Uta

Journal:

Journal of Physics A Mathematical and Theoretical

Year:

2018

Language:

english

File:

PDF, 1.23 MB

english, 2018

8

Energy, ropelength, and other physical aspects of equilateral knots

Kenneth C. Millett, Eric J. Rawdon

Journal:

Journal of Computational Physics

Year:

2003

Language:

english

File:

PDF, 411 KB

english, 2003

9

All Monofilament Knots Assume Sliding Conformation In Vivo

Davis, Daniel A., Pellowski, Donna M., Rawdon, Eric J.

Journal:

Dermatologic Surgery

Year:

2013

Language:

english

File:

PDF, 221 KB

english, 2013

10

Knot localization in proteins

Rawdon, Eric J., Millett, Kenneth C., Sułkowska, Joanna I., Stasiak, Andrzej

Journal:

Biochemical Society Transactions

Year:

2013

Language:

english

File:

PDF, 300 KB

english, 2013

11

Identifying knots in proteins

Millett, Kenneth C., Rawdon, Eric J., Stasiak, Andrzej, Sułkowska, Joanna I.

Journal:

Biochemical Society Transactions

Year:

2013

Language:

english

File:

PDF, 269 KB

english, 2013

12

Conservation of Complex Knotting and Slipknotting Patterns in Proteins

Sulkowska, Joanna I., Rawdon, Eric J., Millet, Kenneth C., Onuchic, Jose N., Stasiak, Andrzej

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 39 KB

english, 2012

13

Scaling Behavior and Equilibrium Lengths of Knotted Polymers

Rawdon, Eric, Dobay, Akos, Kern, John C., Millett, Kenneth C., Piatek, Michael, Plunkett, Patrick, Stasiak, Andrzej

Journal:

Year:

2008

Language:

english

File:

PDF, 268 KB

english, 2008

14

Total Curvature and Total Torsion of Knotted Polymers

Plunkett, Patrick, Piatek, Michael, Dobay, Akos, Kern, John C., Millett, Kenneth C., Stasiak, Andrzej, Rawdon, Eric J.

Journal:

Year:

2007

Language:

english

File:

PDF, 313 KB

english, 2007

15

Effect of Knotting on the Shape of Polymers

Rawdon, Eric J., Kern, John C., Piatek, Michael, Plunkett, Patrick, Stasiak, Andrzej, Millett, Kenneth C.

Journal:

Year:

2008

Language:

english

File:

PDF, 1.33 MB

english, 2008

16

Role of flexibility in entanglement

Buck, Gregory, Rawdon, Eric J.

Journal:

Physical Review E

Year:

2004

Language:

english

File:

PDF, 295 KB

english, 2004

17

Can Computers Discover Ideal Knots?

Rawdon, Eric J.

Journal:

Experimental Mathematics

Year:

2003

Language:

english

File:

PDF, 8.71 MB

english, 2003

18

Knot Tightening by Constrained Gradient Descent

Ashton, Ted, Cantarella, Jason, Piatek, Michael, Rawdon, Eric J.

Journal:

Experimental Mathematics

Year:

2011

Language:

english

File:

PDF, 1.62 MB

english, 2011

19

Tight knot spectrum in QCD

Buniy, Roman V., Cantarella, Jason, Kephart, Thomas W., Rawdon, Eric J.

Journal:

Physical Review D

Year:

2014

Language:

english

File:

PDF, 1.22 MB

english, 2014

20

POLYGONAL KNOT SPACE NEAR ROPELENGTH-MINIMIZED KNOTS

MILLETT, KENNETH C., PIATEK, MICHAEL, RAWDON, ERIC J.

Journal:

Journal of Knot Theory and Its Ramifications

Year:

2008

Language:

english

File:

PDF, 424 KB

english, 2008

21

ERROR ANALYSIS OF THE MINIMUM DISTANCE ENERGY OF A POLYGONAL KNOT AND THE MÖBIUS ENERGY OF AN APPROXIMATING CURVE

RAWDON, ERIC J., WORTHINGTON, JOSEPH

Journal:

Journal of Knot Theory and Its Ramifications

Year:

2010

Language:

english

File:

PDF, 312 KB

english, 2010

22

APPROXIMATING SMOOTH THICKNESS

RAWDON, ERIC J.

Journal:

Journal of Knot Theory and Its Ramifications

Year:

2000

Language:

english

File:

PDF, 2.79 MB

english, 2000

23

POLYGONAL APPROXIMATION AND ENERGY OF SMOOTH KNOTS

RAWDON, ERIC J., SIMON, JONATHAN K.

Journal:

Journal of Knot Theory and Its Ramifications

Year:

2006

Language:

english

File:

PDF, 326 KB

english, 2006

24

Link lengths and their growth powers

Huh, Youngsik, No, Sungjong, Oh, Seungsang, Rawdon, Eric J

Journal:

Journal of Physics A Mathematical and Theoretical

Year:

2015

Language:

english

File:

PDF, 473 KB

english, 2015

25

Shapes of tight composite knots

Cantarella, Jason, LaPointe, Al, Rawdon, Eric J

Journal:

Journal of Physics A Mathematical and Theoretical

Year:

2012

Language:

english

File:

PDF, 739 KB

english, 2012

26

Subknots in ideal knots, random knots, and knotted proteins

Rawdon, Eric J., Millett, Kenneth C., Stasiak, Andrzej

Journal:

Scientific Reports

Year:

2015

Language:

english

File:

PDF, 863 KB

english, 2015

27

Symmetry-breaking in cumulative measures of shapes of polymer models

Millett, Kenneth C., Rawdon, Eric J., Tran, Vy T., Stasiak, Andrzej

Journal:

The Journal of Chemical Physics

Year:

2010

Language:

english

File:

PDF, 1.82 MB

english, 2010

28

Publisher’s Note: “Symmetry-breaking in cumulative measures of shapes of polymer models” [J. Chem. Phys. 133, 154113 (2010)]

Millett, Kenneth C., Rawdon, Eric J., Tran, Vy T., Stasiak, Andrzej

Journal:

The Journal of Chemical Physics

Year:

2010

Language:

english

File:

PDF, 361 KB

english, 2010

29

How topoisomerase IV can efficiently unknot and decatenate negatively supercoiled DNA molecules without causing their torsional relaxation

Rawdon, Eric J., Dorier, Julien, Racko, Dusan, Millett, Kenneth C., Stasiak, Andrzej

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 3.13 MB

english, 2016

30

The spectrum of tightly knotted flux tubes in QCD

Buniy, Roman V, Cantarella, Jason, Kephart, Thomas W, Rawdon, Eric

Journal:

Journal of Physics Conference Series

Year:

2014

Language:

english

File:

PDF, 772 KB

english, 2014

31

LinkProt: a database collecting information about biological links

Dabrowski-Tumanski, Pawel, Jarmolinska, Aleksandra I., Niemyska, Wanda, Rawdon, Eric J., Millett, Kenneth C., Sulkowska, Joanna I.

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 1.44 MB

english, 2016

32

Effect of knotting on polymer shapes and their enveloping ellipsoids

Millett, Kenneth C., Plunkett, Patrick, Piatek, Michael, Rawdon, Eric J., Stasiak, Andrzej

Journal:

The Journal of Chemical Physics

Year:

2009

Language:

english

File:

PDF, 591 KB

english, 2009

33

Sedimentation of macroscopic rigid knots and its relation to gel electrophoretic mobility of DNA knots

Weber, Cédric, Carlen, Mathias, Dietler, Giovanni, Rawdon, Eric J., Stasiak, Andrzej

Journal:

Scientific Reports

Year:

2013

Language:

english

File:

PDF, 1.83 MB

english, 2013

34

Relative Frequencies of Alternating and Nonalternating Prime Knots and Composite Knots in Random Knot Spaces

Diao, Yuanan, Ernst, Claus, Rawdon, Eric J., Ziegler, Uta

Journal:

Experimental Mathematics

Year:

2017

Language:

english

File:

PDF, 1.90 MB

english, 2017

35

Knot fertility and lineage

Cantarella, Jason, Henrich, Allison, Magness, Elsa, O’Keefe, Oliver, Perez, Kayla, Rawdon, Eric, Zimmer, Briana

Journal:

Journal of Knot Theory and Its Ramifications

Year:

2017

Language:

english

File:

PDF, 440 KB

english, 2017

36

Average crossing number and writhe of knotted random polygons in confinement

Diao, Yuanan, Ernst, Claus, Rawdon, Eric J., Ziegler, Uta

Journal:

Reactive and Functional Polymers

Year:

2018

Language:

english

File:

PDF, 2.92 MB

english, 2018