Literature DB >> 19121703

Minimal models for proteins and RNA from folding to function.

David L Pincus1, Samuel S Cho, Changbong Hyeon, D Thirumalai.   

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Year:  2008        PMID： 19121703     DOI： 10.1016/S0079-6603(08)00406-6

Source DB:  PubMed          Journal:  Prog Mol Biol Transl Sci        ISSN： 1877-1173            Impact factor:   3.622


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  15 in total

1.  The origin of nonmonotonic complex behavior and the effects of nonnative interactions on the diffusive properties of protein folding.

Authors:  Ronaldo J Oliveira; Paul C Whitford; Jorge Chahine; Jin Wang; José N Onuchic; Vitor B P Leite
Journal:  Biophys J       Date:  2010-07-21       Impact factor: 4.033

2.  Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways.

Authors:  Paul C Whitford; Peter Geggier; Roger B Altman; Scott C Blanchard; José N Onuchic; Karissa Y Sanbonmatsu
Journal:  RNA       Date:  2010-04-28       Impact factor: 4.942

Review 3.  Modeling nucleic acids.

Authors:  Adelene Y L Sim; Peter Minary; Michael Levitt
Journal:  Curr Opin Struct Biol       Date:  2012-04-25       Impact factor: 6.809

4.  Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures.

Authors:  Samuel S Cho; David L Pincus; D Thirumalai
Journal:  Proc Natl Acad Sci U S A       Date:  2009-10-05       Impact factor: 11.205

5.  Denaturants Alter the Flux through Multiple Pathways in the Folding of PDZ Domain.

Authors:  Zhenxing Liu; D Thirumalai
Journal:  J Phys Chem B       Date:  2018-01-22       Impact factor: 2.991

6.  Collapse kinetics and chevron plots from simulations of denaturant-dependent folding of globular proteins.

Authors:  Zhenxing Liu; Govardhan Reddy; Edward P O'Brien; D Thirumalai
Journal:  Proc Natl Acad Sci U S A       Date:  2011-04-21       Impact factor: 11.205

7.  Coarse-graining RNA nanostructures for molecular dynamics simulations.

Authors:  Maxim Paliy; Roderick Melnik; Bruce A Shapiro
Journal:  Phys Biol       Date:  2010-06-24       Impact factor: 2.583

8.  Crowding effects on the mechanical stability and unfolding pathways of ubiquitin.

Authors:  David L Pincus; D Thirumalai
Journal:  J Phys Chem B       Date:  2009-01-08       Impact factor: 2.991

9.  SMOG@ctbp: simplified deployment of structure-based models in GROMACS.

Authors:  Jeffrey K Noel; Paul C Whitford; Karissa Y Sanbonmatsu; José N Onuchic
Journal:  Nucleic Acids Res       Date:  2010-06-04       Impact factor: 16.971

10.  Searching target sites on DNA by proteins: Role of DNA dynamics under confinement.

Authors:  Anupam Mondal; Arnab Bhattacherjee
Journal:  Nucleic Acids Res       Date:  2015-09-22       Impact factor: 16.971
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