Dunbrack, Roland L: search on Z-Library

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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

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

4

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

5

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

6

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

7

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

8

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

9

Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling

Jo, Sunhwan, Lee, Hui Sun, Skolnick, Jeffrey, Im, Wonpil, Dunbrack, Roland L.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.81 MB

english, 2013

10

Defects in DNA Repair Genes Predict Response to Neoadjuvant Cisplatin-based chemotherapy in Muscle-invasive Bladder Cancer

Plimack, Elizabeth R., Dunbrack, Roland L., Brennan, Timothy A., Andrake, Mark D., Zhou, Yan, Serebriiskii, Ilya G., Slifker, Michael, Alpaugh, Katherine, Dulaimi, Essel, Palma, Norma, Hoffman-Censits

Journal:

European Urology

Year:

2015

Language:

english

File:

PDF, 2.00 MB

english, 2015

11

Charge Asymmetry in Outer Membrane Proteins

Slusky, Joanna, Dunbrack, Roland

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 60 KB

english, 2015

12

CASP 11 Target Classification

Kinch, Lisa N., Li, Wenlin, Schaeffer, R. Dustin, Dunbrack, Roland L., Monastyrskyy, Bohdan, Kryshtafovych, Andriy, Grishin, Nick V.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2016

Language:

english

File:

PDF, 998 KB

english, 2016

13

Exploring E-cadherin-peptidomimetics interaction using NMR and computational studies

Civera, Monica, Vasile, Francesca, Potenza, Donatella, Colombo, Cinzia, Parente, Sara, Vettraino, Chiara, Prosdocimi, Tommaso, Parisini, Emilio, Belvisi, Laura, Dunbrack, Roland L.

Journal:

PLoS Computational Biology

Year:

2019

File:

PDF, 1.46 MB

2019

14

A scoundrel's refuge

Dunbrack, Roland L

Journal:

Natural Structural Biology

Year:

2003

Language:

english

File:

PDF, 111 KB

english, 2003

15

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

16

Neighbor-Dependent Ramachandran Probability Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process Model

Ting, Daniel, Wang, Guoli, Shapovalov, Maxim, Mitra, Rajib, Jordan, Michael I., Dunbrack, Roland L., Richardson, Jane

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.93 MB

english, 2010

17

Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?

Petrov, Drazen, Zagrovic, Bojan, Dunbrack, Roland L.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.23 MB

english, 2014

18

High GC content causes orphan proteins to be intrinsically disordered

Basile, Walter, Sachenkova, Oxana, Light, Sara, Elofsson, Arne, Dunbrack, Roland L.

Journal:

PLoS Computational Biology

Year:

2017

Language:

english

File:

PDF, 3.03 MB

english, 2017

19

Porphobilinogen Synthase from Pea: Expression from an Artificial Gene, Kinetic Characterization, and Novel Implications for Subunit Interactions †

Kervinen, Jukka, Dunbrack, Roland L., Litwin, Samuel, Martins, Jacob, Scarrow, Robert C., Volin, Marina, Yeung, Anthony T., Yoon, Erica, Jaffe, Eileen K.

Journal:

Year:

2000

Language:

english

File:

PDF, 271 KB

english, 2000

20

Genome-Wide Prediction and Validation of Peptides That Bind Human Prosurvival Bcl-2 Proteins

DeBartolo, Joe, Taipale, Mikko, Keating, Amy E., Dunbrack, Roland L.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.05 MB

english, 2014

21

Biological function derived from predicted structures in CASP11

Huwe, Peter J., Xu, Qifang, Shapovalov, Maxim V., Modi, Vivek, Andrake, Mark D., Dunbrack, Roland L.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2016

Language:

english

File:

PDF, 1.63 MB

english, 2016

22

Role of a selecting ligand in shaping the murine γδ-TCR repertoire

Fahl, Shawn P., Coffey, Francis, Kain, Lisa, Zarin, Payam, Dunbrack, Roland L., Teyton, Luc, Zúñiga-Pflücker, Juan Carlos, Kappes, Dietmar J., Wiest, David L.

Journal:

Proceedings of the National Academy of Sciences

Year:

2018

Language:

english

File:

PDF, 1.22 MB

english, 2018

23

Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours

Jumper, John M., Faruk, Nabil F., Freed, Karl F., Sosnick, Tobin R., Dunbrack, Roland L.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.62 MB

english, 2018

24

Protein modeling to assess the pathogenicity of rare variants of SERPINA1 in patients suspected of having Alpha 1 Antitrypsin Deficiency

Kueppers, Friedrich, Andrake, Mark D., Xu, Qifang, Dunbrack, Roland L., Kim, Joannah, Sanders, Christopher L.

Journal:

BMC Medical Genetics

Year:

2019

File:

PDF, 1.58 MB

2019

25

Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD:KRas protein-protein interface

Lowegard, Anna U., Frenkel, Marcel S., Holt, Graham T., Jou, Jonathan D., Ojewole, Adegoke A., Donald, Bruce R., Dunbrack, Roland L.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 10.55 MB

2020

26

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

27

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

28

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

29

Using Entropy Maximization to Understand the Determinants of Structural Dynamics beyond Native Contact Topology

Lezon, Timothy R., Bahar, Ivet, Dunbrack, Roland L.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 620 KB

english, 2010

30

The Origin of CDR H3 Structural Diversity

Weitzner, Brian D., Dunbrack, Roland L., Gray, Jeffrey J.

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 42 KB

english, 2015

31

Mouse modeling and structural analysis of the p.G307S mutation in human cystathionine β-synthase ( CBS ) reveal effects on CBS activity but not stability

Gupta, Sapna, Kelow, Simon, Wang, Liqun, Andrake, Mark, Dunbrack, Roland L., Kruger, Warren D.

Journal:

Journal of Biological Chemistry

Year:

2018

Language:

english

File:

PDF, 6.33 MB

english, 2018

32

ProtCID: a data resource for structural information on protein interactions

Xu, Qifang, Dunbrack, Roland L.

Journal:

Nature Communications

Year:

2020

File:

PDF, 5.20 MB

2020

33

The evolutionarily conserved Dim1 protein defines a novel branch of the thioredoxin fold superfamily

ZHANG, YU-ZHU, GOULD, KATHLEEN L., DUNBRACK, ROLAND L., CHENG, HONG, RODER, HEINRICH, GOLEMIS, ERICA A.

Journal:

Physiological Genomics

Year:

1999

Language:

english

File:

PDF, 612 KB

english, 1999

34

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

35

An Atlas of the Thioredoxin Fold Class Reveals the Complexity of Function-Enabling Adaptations

Atkinson, Holly J., Babbitt, Patricia C., Dunbrack, Roland

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 2.65 MB

english, 2009

36

The Origin of CDR H3 Structural Diversity

Weitzner, Brian D., Dunbrack, Roland L., Gray, Jeffrey J.

Journal:

Year:

2015

Language:

english

File:

PDF, 2.39 MB

english, 2015

37

A Combinatorial Approach to Detect Coevolved Amino Acid Networks in Protein Families of Variable Divergence

Baussand, Julie, Carbone, Alessandra, Dunbrack, Roland

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.14 MB

english, 2009

38

Proportionality: A Valid Alternative to Correlation for Relative Data

Lovell, David, Pawlowsky-Glahn, Vera, Egozcue, Juan José, Marguerat, Samuel, Bähler, Jürg, Dunbrack Jr., Roland L.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 356 KB

english, 2015

39

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

40

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

41

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

42

Network and Atomistic Simulations Unveil the Structural Determinants of Mutations Linked to Retinal Diseases

Mariani, Simona, Dell'Orco, Daniele, Felline, Angelo, Raimondi, Francesco, Fanelli, Francesca, Dunbrack, Roland L.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.75 MB

english, 2013

43

Machines vs. Ensembles: Effective MAPK Signaling through Heterogeneous Sets of Protein Complexes

Suderman, Ryan, Deeds, Eric J., Dunbrack, Roland L.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 906 KB

english, 2013

44

Will Widgets and Semantic Tagging Change Computational Biology?

Bourne, Philip E., Beran, Bojan, Bi, Chunxiao, Bluhm, Wolfgang, Dunbrack, Roland, Prlić, Andreas, Quinn, Greg, Rose, Peter, Shah, Raship, Tao, Wendy, Weitzner, Brian, Yukich, Ben, Nussinov, Ruth

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 432 KB

english, 2010

45

NIH Public Access

North, Benjamin, Lehmann, Andreas, Jr, Roland L Dunbrack

Year:

2012

Language:

english

File:

PDF, 1.11 MB

english, 2012

46

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

47

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

48

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

49

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

50

Improving Contact Prediction along Three Dimensions

Feinauer, Christoph, Skwark, Marcin J., Pagnani, Andrea, Aurell, Erik, Dunbrack, Roland L.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.53 MB

english, 2014

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