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1

Rotamer Libraries in the 21st Century

Roland L Dunbrack Jr.

Journal:

Current Opinion in Structural Biology

Year:

2002

Language:

english

File:

PDF, 100 KB

english, 2002

2

Calculation of Franck-Condon factors for undergraduate quantum chemistry

Dunbrack, Roland L.

Journal:

Journal of Chemical Education

Year:

1986

Language:

english

File:

PDF, 2.53 MB

english, 1986

3

Clinical Trials That Explicitly Exclude Gay and Lesbian Patients

Egleston, Brian L., Dunbrack, Roland L., Hall, Michael J.

Journal:

Boston Medical and Surgical Journal

Year:

2010

Language:

english

File:

PDF, 78 KB

english, 2010

4

TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions

Cang, Zixuan, Wei, Guo-Wei, Dunbrack, Roland L.

Journal:

PLoS Computational Biology

Year:

2017

Language:

english

File:

PDF, 9.02 MB

english, 2017

5

Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases

Kaiser, Florian, Bittrich, Sebastian, Salentin, Sebastian, Leberecht, Christoph, Haupt, V. Joachim, Krautwurst, Sarah, Schroeder, Michael, Labudde, Dirk, Dunbrack, Roland L.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 8.13 MB

english, 2018

6

Comparative modeling of CASP3 targets using PSI-BLAST and SCWRL

Roland L. Dunbrack Jr.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 102 KB

english, 1999

7

Large-scale comparison of protein sequence alignment algorithms with structure alignments

J. Michael Sauder, Jonathan W. Arthur, Roland L. Dunbrack Jr.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2000

Language:

english

File:

PDF, 288 KB

english, 2000

8

OVCA2 is downregulated and degraded during retinoid-induced apoptosis

Amanda H. Prowse, Lisa Vanderveer, Simon W.F. Milling, Zhong-Zong Pan, Roland L. Dunbrack, Xiang-Xi Xu, Andrew K. Godwin

Journal:

International Journal of Cancer

Year:

2002

Language:

english

File:

PDF, 813 KB

english, 2002

9

PONDR-FIT: A meta-predictor of intrinsically disordered amino acids

Bin Xue, Roland L. Dunbrack, Robert W. Williams, A. Keith Dunker, Vladimir N. Uversky

Journal:

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

Year:

2010

Language:

english

File:

PDF, 2.44 MB

english, 2010

10

Bayesian statistical analysis of protein side-chain rotamer preferences

Roland L. Dunbrack Jr., Fred E. Cohen

Journal:

Protein Science

Year:

1997

Language:

english

File:

PDF, 7.44 MB

english, 1997

11

CAFASP2: The second critical assessment of fully automated structure prediction methods

Daniel Fischer, Arne Elofsson, Leszek Rychlewski, Florencio Pazos, Alfonso Valencia, Burkhard Rost, Angel R. Ortiz, Roland L. Dunbrack Jr.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2001

Language:

english

File:

PDF, 378 KB

english, 2001

12

CAFASP3: The third critical assessment of fully automated structure prediction methods

Daniel Fischer, Leszek Rychlewski, Roland L. Dunbrack Jr., Angel R. Ortiz, Arne Elofsson

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 1.68 MB

english, 2003

13

Assessment of fold recognition predictions in CASP6

Guoli Wang, Yumi Jin, Roland L. Dunbrack Jr.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 1.17 MB

english, 2005

14

Assessment of disorder predictions in CASP6

Yumi Jin, Roland L. Dunbrack Jr.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 368 KB

english, 2005

15

Domain definition and target classification for CASP6

Michael Tress, Chin-Hsien Tai, Guoli Wang, Iakes Ezkurdia, Gonzalo López, Alfonso Valencia, Byungkook Lee, Roland L. Dunbrack Jr.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 473 KB

english, 2005

16

Statistical and conformational analysis of the electron density of protein side chains

Maxim V. Shapovalov, Roland L. Dunbrack Jr.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2007

Language:

english

File:

PDF, 2.67 MB

english, 2007

17

An unusually small dimer interface is observed in all available crystal structures of cytosolic sulfotransferases

Brian Weitzner, Thomas Meehan, Qifang Xu, Roland L. Dunbrack Jr.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2009

Language:

english

File:

PDF, 327 KB

english, 2009

18

Improved prediction of protein side-chain conformations with SCWRL4

Georgii G. Krivov, Maxim V. Shapovalov, Roland L. Dunbrack Jr.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2009

Language:

english

File:

PDF, 742 KB

english, 2009

19

Testing computational prediction of missense mutation phenotypes: Functional characterization of 204 mutations of human cystathionine beta synthase

Qiong Wei, Liqun Wang, Qiang Wang, Warren D. Kruger, Roland L. Dunbrack Jr.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 682 KB

english, 2010

20

Minimal ensembles of side chain conformers for modeling protein–protein interactions

Dmitri Beglov, David R. Hall, Ryan Brenke, Maxim V. Shapovalov, Roland L. Dunbrack Jr., Dima Kozakov, Sandor Vajda

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2012

Language:

english

File:

PDF, 1.57 MB

english, 2012

21

Mutational Analysis of the Structure and Function of the CD4 Protein

Carolyn Doyle, Jaekyoon Shin, Roland L. Dunbrack Jr., Jack L. Strominger

Journal:

Immunological Reviews

Year:

1989

Language:

english

File:

PDF, 6.23 MB

english, 1989

22

SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling

Wang, Qiang, Canutescu, Adrian A, Dunbrack, Roland L

Journal:

Nature Protocols

Year:

2008

Language:

english

File:

PDF, 1.14 MB

english, 2008

23

Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains

Dunbrack, Roland L., Karplus, Martin

Journal:

Natural Structural Biology

Year:

1994

File:

PDF, 786 KB

1994

24

A scoundrel's refuge

Dunbrack, Roland L

Journal:

Natural Structural Biology

Year:

2003

Language:

english

File:

PDF, 111 KB

english, 2003

25

Structure of a human ASF1a–HIRA complex and insights into specificity of histone chaperone complex assembly

Tang, Yong, Poustovoitov, Maxim V, Zhao, Kehao, Garfinkel, Megan, Canutescu, Adrian, Dunbrack, Roland, Adams, Peter D, Marmorstein, Ronen

Journal:

Nature Structural and Molecular Biology

Year:

2006

Language:

english

File:

PDF, 617 KB

english, 2006

26

Scoring profile-to-profile sequence alignments

Guoli Wang, Roland L. Dunbrack Jr.

Journal:

Protein Science

Year:

2004

Language:

english

File:

PDF, 576 KB

english, 2004

27

Entamoeba histolytica:Computer-Assisted Modeling of Phosphofructokinase for the Prediction of Broad-Spectrum Antiparasitic Agents

Carrie L. Byington, Roland L. Dunbrack Jr., Frank G. Whitby, Fred E. Cohen, Nina Agabian

Journal:

Experimental Parasitology

Year:

1997

Language:

english

File:

PDF, 335 KB

english, 1997

28

Sequence comparison and protein structure prediction

Roland L Dunbrack Jr

Journal:

Current Opinion in Structural Biology

Year:

2006

Language:

english

File:

PDF, 183 KB

english, 2006

29

Outcome of a Workshop on Archiving Structural Models of Biological Macromolecules

Helen M. Berman, Stephen K. Burley, Wah Chiu, Andrej Sali, Alexei Adzhubei, Philip E. Bourne, Stephen H. Bryant, Roland L. Dunbrack Jr., Krzysztof Fidelis, Joachim Frank, Adam Godzik, Kim Henrick, And

Journal:

Year:

2006

Language:

english

File:

PDF, 162 KB

english, 2006

30

Outcome of a Workshop on Applications of Protein Models in Biomedical Research

Torsten Schwede, Andrej Sali, Barry Honig, Michael Levitt, Helen M. Berman, David Jones, Steven E. Brenner, Stephen K. Burley, Rhiju Das, Nikolay V. Dokholyan, Roland L. Dunbrack Jr., Krzysztof Fideli

Journal:

Year:

2009

Language:

english

File:

PDF, 249 KB

english, 2009

31

Conformation Dependence of Backbone Geometry in Proteins

Donald S. Berkholz, Maxim V. Shapovalov, Roland L. Dunbrack Jr., P. Andrew Karplus

Journal:

Year:

2009

Language:

english

File:

PDF, 1.01 MB

english, 2009

32

A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions

Maxim V. Shapovalov, Roland L. Dunbrack Jr.

Journal:

Year:

2011

Language:

english

File:

PDF, 2.92 MB

english, 2011

33

Chiral N-substituted glycines can form stable helical conformations

Philippe Armand, Kent Kirshenbaum, Alexis Falicov, Roland L Dunbrack Jr, Ken A Dill, Ronald N Zuckermann, Fred E Cohen

Journal:

Folding and Design

Year:

1997

Language:

english

File:

PDF, 625 KB

english, 1997

34

Meeting review: the Second Meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP2), Asilomar, California, December 13–16, 1996

Roland L Dunbrack Jr, Dietlind L Gerloff, Michael Bower, Xiaowu Chen, Olivier Lichtarge, Fred E Cohen

Journal:

Folding and Design

Year:

1997

Language:

english

File:

PDF, 523 KB

english, 1997

35

Aurora A kinase (AURKA) in normal and pathological cell division

Nikonova, Anna S., Astsaturov, Igor, Serebriiskii, Ilya G., Dunbrack, Roland L., Golemis, Erica A.

Journal:

Cellular and Molecular Life Sciences

Year:

2013

Language:

english

File:

PDF, 1.34 MB

english, 2013

36

Ier5,a Novel Member of the Slow-Kinetics Immediate-Early Genes

Max Williams, Myung-Soo Lyu, Yun-Liang Yang, Edward P. Lin, Roland Dunbrack, Bruce Birren, James Cunningham, Kent Hunter

Journal:

Year:

1999

Language:

english

File:

PDF, 240 KB

english, 1999

37

Identification and Structural Analysis of Human RBM8A and RBM8B: Two Highly Conserved RNA-Binding Motif Proteins That Interact with OVCA1, a Candidate Tumor Suppressor

Ana M. Salicioni, Mingrong Xi, Lisa A. Vanderveer, Binaifer Balsara, Joseph R. Testa, Roland L. Dunbrack Jr., Andrew K. Godwin

Journal:

Year:

2000

Language:

english

File:

PDF, 631 KB

english, 2000

38

Identification and Characterization of a Paralog of Human Cell Cycle Checkpoint Gene HUS1

Haiying Hang, Yuzhu Zhang, Roland L. Dunbrack Jr., Cuidong Wang, Howard B. Lieberman

Journal:

Year:

2002

Language:

english

File:

PDF, 293 KB

english, 2002

39

Backbone-dependent Rotamer Library for Proteins Application to Side-chain Prediction

Roland L. Dunbrack Jr, Martin Karplus

Journal:

Journal of Molecular Biology

Year:

1993

File:

PDF, 1.68 MB

1993

40

Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool

Michael J. Bower, Fred E. Cohen, Roland L. Dunbrack Jr

Journal:

Journal of Molecular Biology

Year:

1997

Language:

english

File:

PDF, 495 KB

english, 1997

41

Modeling of substrate specificity of the Alzheimer’s disease amyloid precursor protein β-secretase

J.Michael Sauder, Jonathan W. Arthur, Roland L. Dunbrack Jr

Journal:

Journal of Molecular Biology

Year:

2000

Language:

english

File:

PDF, 790 KB

english, 2000

42

Formation of MacroH2A-Containing Senescence-Associated Heterochromatin Foci and Senescence Driven by ASF1a and HIRA

Rugang Zhang, Maxim V. Poustovoitov, Xiaofen Ye, Hidelita A. Santos, Wei Chen, Sally M. Daganzo, Jan P. Erzberger, Ilya G. Serebriiskii, Adrian A. Canutescu, Roland L. Dunbrack, John R. Pehrson, James

Journal:

Developmental Cell

Year:

2005

Language:

english

File:

PDF, 683 KB

english, 2005

43

Statistical Analysis of Interface Similarity in Crystals of Homologous Proteins

Qifang Xu, Adrian A. Canutescu, Guoli Wang, Maxim Shapovalov, Zoran Obradovic, Roland L. Dunbrack Jr

Journal:

Journal of Molecular Biology

Year:

2008

Language:

english

File:

PDF, 1.91 MB

english, 2008

44

A New Clustering of Antibody CDR Loop Conformations

Benjamin North, Andreas Lehmann, Roland L. Dunbrack Jr

Journal:

Journal of Molecular Biology

Year:

2011

Language:

english

File:

PDF, 2.26 MB

english, 2011

45

The Sanpodo NPAF motif is required for Numb-mediated endocytosis but not Notch signaling regulation in Drosophila

Fabrice Roegiers, Diana Zitserman, Ilya Serebriiskii, Mark Andrake, Roland Dunbrack, Xin Tong

Journal:

Developmental Biology

Year:

2009

Language:

english

File:

PDF, 61 KB

english, 2009

46

A new model for allosteric regulation of phenylalanine hydroxylase: Implications for disease and therapeutics

Jaffe, Eileen K., Stith, Linda, Lawrence, Sarah H., Andrake, Mark, Dunbrack, Roland L.

Journal:

Archives of Biochemistry and Biophysics

Year:

2013

Language:

english

File:

PDF, 1.74 MB

english, 2013

47

Protein-intrinsic and signaling network-based sources of resistance to EGFR- and ErbB family-targeted therapies in head and neck cancer

Ranee Mehra, Ilya G. Serebriiskii, Roland L. Dunbrack Jr., Matthew K. Robinson, Barbara Burtness, Erica A. Golemis

Journal:

Drug Resistance Updates

Year:

2011

Language:

english

File:

PDF, 2.13 MB

english, 2011

48

Prediction of phenotypes of missense mutations in human proteins from biological assemblies

Wei, Qiong, Xu, Qifang, Dunbrack, Roland L.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2013

Language:

english

File:

PDF, 2.81 MB

english, 2013

49

Cyclic coordinate descent: A robotics algorithm for protein loop closure

Adrian A. Canutescu, Roland L. Dunbrack Jr.

Journal:

Protein Science

Year:

2003

Language:

english

File:

PDF, 517 KB

english, 2003

50

A graph-theory algorithm for rapid protein side-chain prediction

Adrian A. Canutescu, Andrew A. Shelenkov, Roland L. Dunbrack Jr.

Journal:

Protein Science

Year:

2003

Language:

english

File:

PDF, 327 KB

english, 2003