Rohit V. Pappu: search on Z-Library

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1

Collapse Transitions of Proteins and the Interplay Among Backbone, Sidechain, and Solvent Interactions

Holehouse, Alex S., Pappu, Rohit V.

Journal:

Annual Review of Biophysics

Year:

2018

Language:

english

File:

PDF, 1.60 MB

english, 2018

2

Tardigrades use intrinsically disordered proteins to survive desiccation

Boothby, Thomas C., Piszkiewicz, Samantha, Holehouse, Alex, Pappu, Rohit V., Pielak, Gary J.

Journal:

Year:

2018

Language:

english

File:

PDF, 68 KB

english, 2018

3

Physical Principles Underlying the Complex Biology of Intracellular Phase Transitions

Choi, Jeong-Mo, Holehouse, Alex S., Pappu, Rohit V.

Journal:

Annual Review of Biophysics

Year:

2020

Language:

english

File:

PDF, 1.55 MB

english, 2020

4

Analysis and Application of Potential Energy Smoothing and Search Methods for Global Optimization

Pappu, Rohit V., Hart, Reece K., Ponder, Jay W.

Journal:

Journal of Physical Chemistry B

Year:

1998

Language:

english

File:

PDF, 288 KB

english, 1998

5

O4-06-07: MMP-9 degrades fibrilllar Abeta in vitro and compact plaques in situ

Jin-Moo Lee, Xiaoyan Hu, Scott Crick, Haowei Song, Kejie Yin, John Cirrito, Randy Bateman, Chung Y. Hsu, Jan Xu, Fong F. Hsu, John Turk, Rohit Pappu, David M. Holtzman, Ping Yan

Journal:

Alzheimer's & Dementia

Year:

2006

Language:

english

File:

PDF, 64 KB

english, 2006

6

An intrinsically disordered linker plays a critical role in bacterial cell division

Buske, P.J., Mittal, Anuradha, Pappu, Rohit V., Levin, Petra Anne

Journal:

Seminars in Cell & Developmental Biology

Year:

2015

Language:

english

File:

PDF, 1.59 MB

english, 2015

7

Coexisting Liquid Phases Underlie Nucleolar Subcompartments

Feric, Marina, Vaidya, Nilesh, Harmon, Tyler S., Mitrea, Diana M., Zhu, Lian, Richardson, Tiffany M., Kriwacki, Richard W., Pappu, Rohit V., Brangwynne, Clifford P.

Journal:

Year:

2016

Language:

english

File:

PDF, 2.73 MB

english, 2016

8

Tardigrade Disordered Proteins Mediate Desiccation Tolerance

Boothby, Thomas C., Piszkiewicz, Samantha, Mehta, Aakash, Brozena, Alexandra, Tapia, Hugo, Koshland, Doug, Holehouse, Alex, Pappu, Rohit, Goldstein, Bob, Pielak, Gary

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 45 KB

english, 2017

9

Simultaneous quantification of protein order and disorder

Sormanni, Pietro, Piovesan, Damiano, Heller, Gabriella T, Bonomi, Massimiliano, Kukic, Predrag, Camilloni, Carlo, Fuxreiter, Monika, Dosztanyi, Zsuzsanna, Pappu, Rohit V, Babu, M Madan, Longhi, Sonia,

Journal:

Nature Chemical Biology

Year:

2017

Language:

english

File:

PDF, 2.51 MB

english, 2017

10

FUS Zigzags Its Way to Cross Beta

Holehouse, Alex S., Pappu, Rohit V.

Journal:

Year:

2017

Language:

english

File:

PDF, 802 KB

english, 2017

11

Gelation and Vitrification of Tardigrade IDPs

Boothby, Thomas C., Piszkiewicz, Samantha, Mehta, Aakash, Brozena, Alexandra, Tapia, Hugo, Koshland, Doug, Holehouse, Alex, Pappu, Rohit, Goldstein, Bob, Pielak, Gary

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 62 KB

english, 2018

12

Electrostatic multipole representation of a polypeptide chain: An algorithm for simulation of polypeptide properties

Pappu, Rohit V., Schneller, William J., Weaver, David L.

Journal:

Journal of Computational Chemistry

Year:

1996

Language:

english

File:

PDF, 1.93 MB

english, 1996

13

Exploring the similarities between potential smoothing and simulated annealing

Hart, Reece K., Pappu, Rohit V., Ponder, Jay W.

Journal:

Journal of Computational Chemistry

Year:

2000

Language:

english

File:

PDF, 438 KB

english, 2000

14

Accuracy of side-chain prediction upon near-native protein backbones generated by ab initio folding methods

Enoch S. Huang, Patrice Koehl, Michael Levitt, Rohit V. Pappu, Jay W. Ponder

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1998

Language:

english

File:

PDF, 212 KB

english, 1998

15

Review of the fourth Johns Hopkins Protein Folding Meeting

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 55 KB

english, 1999

16

Amyloids Go Genomic: Insights Regarding the Sequence Determinants of Prion Formation from Genome-Wide Studies

Hilal A. Lashuel, Rohit V. Pappu

Journal:

Year:

2009

Language:

english

File:

PDF, 598 KB

english, 2009

17

ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutions

Andreas Vitalis, Rohit V. Pappu

Journal:

Journal of Computational Chemistry

Year:

2009

Language:

english

File:

PDF, 1.03 MB

english, 2009

18

Exact recording of Metropolis–Hastings-class Monte Carlo simulations using one bit per sample

Albert H. Mao, Rohit V. Pappu

Journal:

Computer Physics Communications

Year:

2011

Language:

english

File:

PDF, 114 KB

english, 2011

19

The early folding kinetics of apomyoglobin

Rohit V. Pappu, David L. Weaver

Journal:

Protein Science

Year:

1998

Language:

english

File:

PDF, 1.68 MB

english, 1998

20

Characterizing the conformational ensemble of monomeric polyglutamine

Xiaoling Wang, Andreas Vitalis, Matthew A. Wyczalkowski, Rohit V. Pappu

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 1.38 MB

english, 2006

21

10.1038/4922

Ponder, Jay W., Pappu, Rohit V., Marshall, Garland R.

Journal:

Natural Structural Biology

Year:

1999

Language:

english

File:

PDF, 346 KB

english, 1999

22

10.1038/5891

Pappu, Rohit V., Marshall, Garland R., Ponder, Jay W.

Journal:

Natural Structural Biology

Year:

1999

Language:

english

File:

PDF, 45 KB

english, 1999

23

Quantitative Characterization of Ion Pairing and Cluster Formation in Strong 1:1 Electrolytes

Chen, Alan A., Pappu, Rohit V.

Journal:

Journal of Physical Chemistry B

Year:

2007

Language:

english

File:

PDF, 403 KB

english, 2007

24

A simple model for polyproline II structure in unfolded states of alanine-based peptides

Rohit V. Pappu, George D. Rose

Journal:

Protein Science

Year:

2002

Language:

english

File:

PDF, 475 KB

english, 2002

25

Assessing the contribution of heterogeneous distributions of oligomers to aggregation mechanisms of polyglutamine peptides

Andreas Vitalis, Rohit V. Pappu

Journal:

Biophysical Chemistry

Year:

2011

Language:

english

File:

PDF, 1.22 MB

english, 2011

26

NanoParticle Ontology for cancer nanotechnology research

Dennis G. Thomas, Rohit V. Pappu, Nathan A. Baker

Journal:

Journal of Biomedical Informatics

Year:

2011

Language:

english

File:

PDF, 3.07 MB

english, 2011

27

Role of Backbone−Solvent Interactions in Determining Conformational Equilibria of Intrinsically Disordered Proteins

Tran, Hoang T., Mao, Albert, Pappu, Rohit V.

Journal:

Journal of the American Chemical Society

Year:

2008

Language:

english

File:

PDF, 1.42 MB

english, 2008

28

A polymer physics perspective on driving forces and mechanisms for protein aggregation

Rohit V. Pappu, Xiaoling Wang, Andreas Vitalis, Scott L. Crick

Journal:

Archives of Biochemistry and Biophysics

Year:

2008

Language:

english

File:

PDF, 655 KB

english, 2008

29

Atomistic Simulations of the Effects of Polyglutamine Chain Length and Solvent Quality on Conformational Equilibria and Spontaneous Homodimerization

Andreas Vitalis, Xiaoling Wang, Rohit V. Pappu

Journal:

Journal of Molecular Biology

Year:

2008

Language:

english

File:

PDF, 1.39 MB

english, 2008

30

Molecular Simulation Studies of Monovalent Counterion-Mediated Interactions in a Model RNA Kissing Loop

Alan A. Chen, David E. Draper, Rohit V. Pappu

Journal:

Journal of Molecular Biology

Year:

2009

Language:

english

File:

PDF, 887 KB

english, 2009

31

Modulation of Polyglutamine Conformations and Dimer Formation by the N-Terminus of Huntingtin

Tim E. Williamson, Andreas Vitalis, Scott L. Crick, Rohit V. Pappu

Journal:

Journal of Molecular Biology

Year:

2010

Language:

english

File:

PDF, 2.04 MB

english, 2010

32

N-Terminal Segments Modulate the α-Helical Propensities of the Intrinsically Disordered Basic Regions of bZIP Proteins

Rahul K. Das, Scott L. Crick, Rohit V. Pappu

Journal:

Journal of Molecular Biology

Year:

2012

Language:

english

File:

PDF, 518 KB

english, 2012

33

Opposing Effects of Glutamine and Asparagine Govern Prion Formation by Intrinsically Disordered Proteins

Randal Halfmann, Simon Alberti, Rajaraman Krishnan, Nicholas Lyle, Charles W. O'Donnell, Oliver D. King, Bonnie Berger, Rohit V. Pappu, Susan Lindquist

Journal:

Year:

2011

Language:

english

File:

PDF, 2.01 MB

english, 2011

34

Role of Solvent in Determining Conformational Preferences of Alanine Dipeptide in Water

Drozdov, Alexander N., Grossfield, Alan, Pappu, Rohit V.

Journal:

Journal of the American Chemical Society

Year:

2004

Language:

english

File:

PDF, 239 KB

english, 2004

35

Describing sequence–ensemble relationships for intrinsically disordered proteins

Mao, Albert H., Lyle, Nicholas, Pappu, Rohit V.

Journal:

Biochemical Journal

Year:

2013

Language:

english

File:

PDF, 922 KB

english, 2013

36

New Estimators for Calculating Solvation Entropy and Enthalpy and Comparative Assessments of Their Accuracy and Precision

Wyczalkowski, Matthew A., Vitalis, Andreas, Pappu, Rohit V.

Journal:

Journal of Physical Chemistry B

Year:

2010

Language:

english

File:

PDF, 2.77 MB

english, 2010

37

Amyloid seeds formed by cellular uptake, concentration, and aggergation of the Abeta1-42 peptide

Jin-Moo Lee, Scott Crick, Rohit Pappu, Carl Frieden, Xiaoyan Hu

Journal:

Alzheimer's & Dementia

Year:

2009

Language:

english

File:

PDF, 42 KB

english, 2009

38

How is functional specificity achieved through disordered regions of proteins?

Das, Rahul K., Mittal, Anuradha, Pappu, Rohit V.

Journal:

Year:

2013

Language:

english

File:

PDF, 182 KB

english, 2013

39

Thermodynamics of β-Sheet Formation in Polyglutamine

Vitalis, Andreas, Lyle, Nicholas, Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 975 KB

english, 2009

40

Conformational Fluctuations within the Intrinsically Disordered RAM Domain of the Notch Receptor are Governed by the Patterning of Charged Residues within the Primary Sequence

Das, Rahul K., Barrick, Doug, Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 36 KB

english, 2011

41

Alterations to the Conformational Ensemble and Intermolecular Associations of Polyglutamine Due to Charged Side Chains at the N- and C-Termini

Lyle, Nicholas J., Crick, Scott L., Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 35 KB

english, 2011

42

Intrinsic Helicity of Disordered Basic Regions of Bzip Transcription Factors: Implications For Mechanisms of DNA Binding

Das, Rahul K., Crick, Scott L., Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 35 KB

english, 2011

43

Inferring Aggregation Mechanisms of Polyglutamine Through Quantitative Studies of Phase Behavior

Crick, Scott L., Mao, Albert H., Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 59 KB

english, 2012

44

Toward an Accurate Theoretical Framework for Describing Ensembles for Proteins under Strongly Denaturing Conditions

Tran, Hoang T., Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2006

Language:

english

File:

PDF, 605 KB

english, 2006

45

Quantitative Characterization of Intrinsic Disorder in Polyglutamine: Insights from Analysis Based on Polymer Theories

Vitalis, Andreas, Wang, Xiaoling, Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2007

Language:

english

File:

PDF, 719 KB

english, 2007

46

Parameters of Monovalent Ions in the AMBER-99 Forcefield: Assessment of Inaccuracies and Proposed Improvements

Chen, Alan A., Pappu, Rohit V.

Journal:

Journal of Physical Chemistry B

Year:

2007

Language:

english

File:

PDF, 137 KB

english, 2007

47

Connecting Sequence to Conformational Properties of Intrinsically Disordered Proteins: A Charged Relationship

Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 69 KB

english, 2013

48

Functional Implications of Intrinsic Helicities within Basic Regions of bZIP Transcription Factors

Das, Rahul K., Ruff, Kiersten, Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 31 KB

english, 2013

49

Announcements

Das, Rahul K., Ruff, Kiersten, Pappu, Rohit V.

Journal:

The American Journal of Emergency Medicine

Year:

1990

Language:

english

File:

PDF, 101 KB

english, 1990

50

Intrinsically Disordered Protein Regions Modeled as Isolated Entities Commonly Adopt Ensembles of Collapsed, Globular Conformations

Mao, Albert H., Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 35 KB

english, 2011