Computational analysis of amino acids and their sidechain analogs in crowded solutions of RNA nucleobases with implications for the mRNA–protein complementarity hypothesis

How cells get the message: dynamic assembly and function of mRNA–protein complexes

(2013) Michaela Müller-McNicoll et al.   NATURE REVIEWS GENETICS

Structure and function of long noncoding RNAs in epigenetic regulation

(2013) Tim R Mercer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein

(2013) Andreas Zanzoni et al.   NUCLEIC ACIDS RESEARCH

Evidence of direct complementary interactions between messenger RNAs and their cognate proteins

(2013) A. A. Polyansky et al.   NUCLEIC ACIDS RESEARCH

Proteome-wide analysis reveals clues of complementary interactions between mRNAs and their cognate proteins as the physicochemical foundation of the genetic code

(2013) Anton A Polyansky et al.   RNA Biology

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

(2012) Alexander G. Baltz et al.   MOLECULAR CELL

Sequence signatures of direct complementarity between mRNAs and cognate proteins on multiple levels

(2012) Mario Hlevnjak et al.   NUCLEIC ACIDS RESEARCH

Update on activities at the Universal Protein Resource (UniProt) in 2013

(2012)   NUCLEIC ACIDS RESEARCH

RNA–protein interactions in vivo: global gets specific

(2012) Minna-Liisa Änkö et al.   TRENDS IN BIOCHEMICAL SCIENCES

DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking

(2011) Irina Tuszynska et al.   BMC BIOINFORMATICS

Computational methods for prediction of protein–RNA interactions

(2011) Tomasz Puton et al.   JOURNAL OF STRUCTURAL BIOLOGY

Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide–protein complexes

(2011) Jiro Kondo et al.   NUCLEIC ACIDS RESEARCH

Pre-mRNA Processing Reaches Back toTranscription and Ahead to Translation

(2009) Melissa J. Moore et al.   CELL

Origin and evolution of the genetic code: The universal enigma

(2009) Eugene V. Koonin et al.   IUBMB LIFE

RNA–Amino Acid Binding: A Stereochemical Era for the Genetic Code

(2009) Michael Yarus et al.   JOURNAL OF MOLECULAR EVOLUTION

RNA processing and its regulation: global insights into biological networks

(2009) Donny D. Licatalosi et al.   NATURE REVIEWS GENETICS

Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters

(2009) M. A. Jonikas et al.   RNA

Interaction between uracil nucleobase and phenylalanine amino acid: the role of sodium cation in stacking

(2009) Ali Ebrahimi et al.   THEORETICAL CHEMISTRY ACCOUNTS

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

On the Physical Basis of the Amino Acid Polar Requirement

(2008) Damien C. Mathew et al.   JOURNAL OF MOLECULAR EVOLUTION

Computational comparison of the stacking interactions between the aromatic amino acids and the natural or (cationic) methylated nucleobases

(2008) Lesley R. Rutledge et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS