Interaction preferences between nucleobase mimetics and amino acids in aqueous solutions

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

(2014) Matea Hajnic et al.   NUCLEIC ACIDS RESEARCH

Absolute binding-free energies between standard RNA/DNA nucleobases and amino-acid sidechain analogs in different environments

(2014) Anita de Ruiter et al.   NUCLEIC ACIDS RESEARCH

Charge Group Partitioning in Biomolecular Simulation

(2013) Stefan Canzar et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

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

(2012) Mario Hlevnjak et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Irina Tuszynska et al.   BMC BIOINFORMATICS

An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0

(2011) Alpeshkumar K. Malde et al.   Journal of Chemical Theory and Computation

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

(2011) Jiro Kondo et al.   NUCLEIC ACIDS RESEARCH

Plasticity of Cytochrome P450 2B4 as Investigated by Hydrogen-Deuterium Exchange Mass Spectrometry and X-ray Crystallography

(2010) P. Ross Wilderman et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Assessing the Stability of Alzheimer’s Amyloid Protofibrils Using Molecular Dynamics

(2010) Justin A. Lemkul et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

On the Physical Basis of the Amino Acid Polar Requirement

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

Investigation of Binding of UDP-Galfand UDP-[3-F]Galfto UDP-galactopyranose Mutase by STD-NMR Spectroscopy, Molecular Dynamics, and CORCEMA-ST Calculations†

(2008) Yue Yuan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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