Ranjan V Mannige

Ranjan V Mannige

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Ranjan V Mannige

Ranjan V Mannige

Publications by authors named "Ranjan V Mannige"

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18Publications

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The Ramachandran Number: An Order Parameter for Protein Geometry.

PLoS One 2016 4;11(8):e0160023. Epub 2016 Aug 4.

Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0160023PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4973960PMC
August 2017

An exhaustive survey of regular peptide conformations using a new metric for backbone handedness ().

Authors:
Ranjan V Mannige

PeerJ 2017 16;5:e3327. Epub 2017 May 16.

Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.

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http://dx.doi.org/10.7717/peerj.3327DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5436576PMC
May 2017

Structure based sequence analysis of viral and cellular protein assemblies.

J Struct Biol 2016 12 29;196(3):299-308. Epub 2016 Jul 29.

Biomolecular Diversity Laboratory, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Mexico. Electronic address:

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http://dx.doi.org/10.1016/j.jsb.2016.07.013DOI Listing
December 2016

Predicting the outcome of the growth of binary solids far from equilibrium.

Phys Rev E 2016 Apr 27;93:042136. Epub 2016 Apr 27.

Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1103/PhysRevE.93.042136DOI Listing
April 2016

Design, Synthesis, Assembly, and Engineering of Peptoid Nanosheets.

Acc Chem Res 2016 Mar 7;49(3):379-89. Epub 2016 Jan 7.

Molecular Foundry, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States.

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http://dx.doi.org/10.1021/acs.accounts.5b00439DOI Listing
March 2016

Landscape of kinetically trapped binary assemblies.

Authors:
Ranjan V Mannige

J Chem Phys 2015 Dec;143(21):214902

Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1063/1.4936266DOI Listing
December 2015

Peptoid nanosheets exhibit a new secondary-structure motif.

Nature 2015 Oct 7;526(7573):415-20. Epub 2015 Oct 7.

Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94709, USA.

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http://dx.doi.org/10.1038/nature15363DOI Listing
October 2015

Heterogeneity of functional groups in a metal-organic framework displays magic number ratios.

Proc Natl Acad Sci U S A 2015 May 21;112(18):5591-6. Epub 2015 Apr 21.

Department of Chemistry, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, CA 94720; Kavli Energy NanoScience Institute, Berkeley, CA 94720

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http://dx.doi.org/10.1073/pnas.1416417112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4426423PMC
May 2015

Modeling sequence-specific polymers using anisotropic coarse-grained sites allows quantitative comparison with experiment.

J Chem Theory Comput 2015 Jan;11(1):303-15

Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.

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http://dx.doi.org/10.1021/ct5010559DOI Listing
January 2015

Growth of equilibrium structures built from a large number of distinct component types.

Soft Matter 2014 Sep;10(34):6404-16

Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1039/c4sm01021cDOI Listing
September 2014

Dynamic New World: Refining Our View of Protein Structure, Function and Evolution.

Authors:
Ranjan V Mannige

Proteomes 2014 Mar 7;2(1):128-153. Epub 2014 Mar 7.

Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road,Berkeley, CA 94720, USA.

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http://dx.doi.org/10.3390/proteomes2010128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5302727PMC
March 2014

Origination of the Protein Fold Repertoire from Oily Pluripotent Peptides.

Authors:
Ranjan V Mannige

Proteomes 2014 Mar 25;2(2):154-168. Epub 2014 Mar 25.

Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720,USA.

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http://dx.doi.org/10.3390/proteomes2020154DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5302733PMC
March 2014

Development and use of an atomistic CHARMM-based forcefield for peptoid simulation.

J Comput Chem 2014 Feb 29;35(5):360-70. Epub 2013 Nov 29.

Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California, 94720.

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http://doi.wiley.com/10.1002/jcc.23478
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http://dx.doi.org/10.1002/jcc.23478DOI Listing
February 2014

Two modes of protein sequence evolution and their compositional dependencies.

Authors:
Ranjan V Mannige

Phys Rev E Stat Nonlin Soft Matter Phys 2013 Jun 24;87(6):062714. Epub 2013 Jun 24.

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

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http://dx.doi.org/10.1103/PhysRevE.87.062714DOI Listing
June 2013

A universal trend among proteomes indicates an oily last common ancestor.

PLoS Comput Biol 2012 27;8(12):e1002839. Epub 2012 Dec 27.

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1002839DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531291PMC
May 2013

Periodic table of virus capsids: implications for natural selection and design.

PLoS One 2010 Mar 4;5(3):e9423. Epub 2010 Mar 4.

Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009423PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2831995PMC
March 2010

Geometric considerations in virus capsid size specificity, auxiliary requirements, and buckling.

Proc Natl Acad Sci U S A 2009 May 13;106(21):8531-6. Epub 2009 May 13.

Department of Molecular Biology and Center for Theoretical Biological Physics, The Scripps Research Institute, 10550 North Torrey Pines Court, TPC 6, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1073/pnas.0811517106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688982PMC
May 2009

Tilable nature of virus capsids and the role of topological constraints in natural capsid design.

Phys Rev E Stat Nonlin Soft Matter Phys 2008 May 1;77(5 Pt 1):051902. Epub 2008 May 1.

Department of Molecular Biology and Center for Theoretical Biological Physics, The Scripps Research Institute, 10550 North Torrey Pines Road, TPC 6, La Jolla, California 92037, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756041PMC
http://dx.doi.org/10.1103/PhysRevE.77.051902DOI Listing
May 2008