Publications ('*' indicates corresponding author[s])

Mannige RV*

The BackMAP python module: how a simpler Ramachandran number can simplify the life of a protein simulator.

PeerJ (2017) 6:e5745 [link|pdf|GitHub].

Mannige RV*

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

PeerJ (2017) 5:e3327 [link|pdf|GitHub].

Montiel-García DJ, Mannige RV, Reddy VS & Carrillo-Tripp M*

Structure based sequence analysis of viral and cellular protein assemblies.

Journal of Structural Biology (2016) in press [link|pdf].

Mannige RV*, Kundu J & Whitelam S*

The Ramachandran number: an order parameter for protein geometry.

PLoS ONE (2016) 11(8):e0160023 [link|pdf].

Mannige RV* & Whitelam S*

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

Physical Review E (2016) 93:042136 [link|pdf].

Robertson EJ, Battigelli A, Proulx C, Mannige RV, Haxon TK, Whitelam S and Zuckermann RN*

Design, Synthesis, and Assembly of Peptoid Nanosheets.

Accounts of Chemical Research (2016) 49:(3)379 [link|pdf].

Journal cover [link]; Most downloaded paper in January [link].

Mannige RV*

Landscape of kinetically trapped binary assemblies.

Journal of Chemical Physics (2015) 143:214902 [link|pdf].

Mannige RV*, Haxton TK, Proulx C, Robertson EJ, Battigelli A, Butterfoss G, Zuckermann RN and Whitelam S* (2015)

Peptoid nanosheets exhibit a new secondary structure motif.

Nature (2015) 526:415 [link|pdf].

Featured by C&E News [link], Berkeley Lab [link] and 8 other news sites [link].

Sue AC-H*, Mannige RV*, Deng H, Cao D, Wang C, Gándara F, Stoddart JF*, Whitelam S* and Yaghi OM*

Two-component metal-organic framework displaying compositional robustness to solution constitution.

Proceedings of the National Academy of Sciences (2015) 112(18):5591 [link|pdf].

*: Equal contribution.

Featured in a Phys.org article [link].

Haxton TK*, Mannige RV, Zuckermann RN and Whitelam S*

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

Journal of Chemical Theory and Computation (2015) 11(1):303 [link|pdf].

Hedges LO, Mannige RV, Whitelam S*

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

Soft Matter (2014) 10(34):6404 [link|pdf].

Journal cover [link]; Featured as a “hot paper” of 2014 [link].

Mannige RV*

Origination of the protein fold repertoire from oily pluripotent peptides.

Proteomes (2014) 2(2):154 [link|pdf].

Mannige RV*

Dynamic new world: refining our view of protein structure, function and evolution.

Proteomes (2014) 2(1):128 [link|pdf].

Figure reused in textbook Introduction to Protein Science (3rd Ed), Arthur Lesk (Author), Oxford University Press.

Mirijanian DT, Mannige RV, Zuckermann RN and Whitelam S*

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

Journal of Computational Chemistry (2014) 35(5):360 [link|pdf].

Journal cover [link]; Featured by the Department of Defense [link]; Mentioned as “important upcoming paper” [link].

Mannige RV*

Two modes of protein sequence evolution and their compositional dependencies.

Physical Review E (2013) 87(6):062714 [link|pdf].

Mannige RV*, Brooks CL III and Shakhnovich EI.

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

PLoS Computational Biology (2012) 8(12):e1002839 [link|pdf].

In the news as a GenomeWeb.com paper of note, 01/25/2013. [link]

May ER, Arora K, Mannige RV, Nguyen H and Brooks CL III*

Multiscale modeling of virus structure, assembly and dynamics.

Chapter in Book: Computational Modeling of Biological Systems: From Molecules to Pathways. (2011) Springer Berlin. ISBN 9781461421450. Ed: Dokholyan, N [link|pdf].

Mannige RV* and Brooks CL III*

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

PLoS ONE (2010) 5(3):e9423 [link|pdf].

Discussed in textbooks:Principles of Molecular Virology, Alan Cann (Author), Academic Press; Nanomedicine (Frontiers of Nanoscience), Huw D Summers (Editor), Elsevier.
Discussed in book for utility of math in biology: The Emergence and Nature of Human History Volume One, Joseph Miller.

Mannige RV

Principles of virus capsid design.

ProQuest Publishing (2010) ISBN # 9781109683769 [link|submitted pdf].

Mannige RV* and Brooks CL III*

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

Proceedings of the National Academy of Sciences (2009) 106(21):8531 [link|pdf].

Mannige RV* and Brooks CL III*

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

Physical Review E (2008) 77(5):051902 [link|pdf].

Feature story by the American Physical Society for advancing structural virology in the article “Piecing a Virus Together”, Phys. Rev. Focus, 21:18. [link]

Mannige RV and Pettitt BM.

P-PIDA: a long-range pattern detection algorithm for proteins.

University of Houston Library (2004) Senior Honors Thesis.

Winner of the University of Houston Outstanding Senior Thesis Award.

© Ranjan Mannige