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

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

New Interaction Parameters for Charged Amino Acid Side Chains in the GROMOS Force Field

(2012) Maria M. Reif et al.   Journal of Chemical Theory and Computation

Evaluating nonpolarizable nucleic acid force fields: A systematic comparison of the nucleobases hydration free energies and chloroform-to-water partition coefficients

(2012) Maarten G. Wolf et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

(2012) Mario Hlevnjak et al.   NUCLEIC ACIDS RESEARCH

On origin of genetic code and tRNA before translation

(2011) Andrei S Rodin et al.   Biology Direct

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

(2011) Irina Tuszynska et al.   BMC BIOINFORMATICS

Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation

(2011) Nathan Schmid et al.   COMPUTER PHYSICS COMMUNICATIONS

Computation of methodology-independent single-ion solvation properties from molecular simulations. III. Correction terms for the solvation free energies, enthalpies, entropies, heat capacities, volumes, compressibilities, and expansivities of solvated ions

(2011) Maria M. Reif et al.   JOURNAL OF CHEMICAL PHYSICS

Effects of Extending the Computational Model on DNA–Protein T-shaped Interactions: The Case of Adenine–Histidine Dimers

(2011) Lesley R. Rutledge et al.   JOURNAL OF PHYSICAL CHEMISTRY A

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

(2011) Jiro Kondo et al.   NUCLEIC ACIDS RESEARCH

Imprints of the genetic code in the ribosome

(2010) D. B. F. Johnson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Hydration Free Energies of Amino Acids: Why Side Chain Analog Data Are Not Enough

(2009) Gerhard König 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

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