Paper by Alexey Onufriev selected as featured article in Nucleic Acids Research

Publish Date: 03/16/2013

Alexey Onufriev's paper, "Automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations," was selected as a featured article in Nucleic Acids Research, a journal with an impact factor of 8. Featured articles in this journal represent the top 5% of NAR papers in terms of originality, significance and scientific excellence. A "lay synopsis" of the article is as follows:

"The accuracy of biomolecular modeling and simulation, such as molecular dynamics (MD) depends on the accuracy of the input structures. Preparing these structures can involve the use of a variety of different tools for: correcting errors, adding missing atoms, filling valances with hydrogens, predicting pK values for titratable amino acids, assigning predefined partial charges and radii to all atoms, and generating force field parameter/topology files. H++ automates the above key steps and performs extensive error and consistency checking, providing error/warning messages together with suggested corrections. H++ is available at"

Onufriev also has a new PNAS (Proceedings of the National Academy of Science) article, "Two-phase stretching of molecular chains." This article reports on work from a US-Russian research collaboration funded by CRDF Global and the Russian Federation for Basic Research. According to the CRDF website:

"The project's goal was to clarify the impacts of nonlinear effects on DNA structural transformations and the formation of its physical and mechanical properties. These properties are important for fundamental understanding of DNA as the basis of heredity and mutagenesis, and thus the existence of congenital diseases and cancer. Potential use of DNA in nanotechnology applications also requires deep understanding of its physical properties at single molecule level, often different from expectation."