Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations
Alkali (Li+, Na+, K+, Rb+, and Cs+) and halide (F−, Cl−, Br−, and I−) ions play an important
role in many biological phenomena, roles that range from stabilization of biomolecular …
role in many biological phenomena, roles that range from stabilization of biomolecular …
Parmbsc1: a refined force field for DNA simulations
We present parmbsc1, a force field for DNA atomistic simulation, which has been
parameterized from high-level quantum mechanical data and tested for nearly 100 systems …
parameterized from high-level quantum mechanical data and tested for nearly 100 systems …
Frontiers in molecular dynamics simulations of DNA
It has been known for decades that DNA is extremely flexible and polymorphic, but our
knowledge of its accessible conformational space remains limited. Structural data, primarily …
knowledge of its accessible conformational space remains limited. Structural data, primarily …
Refinement of the AMBER force field for nucleic acids: improving the description of α/γ conformers
We present here the parmbsc0 force field, a refinement of the AMBER parm99 force field,
where emphasis has been made on the correct representation of the α/γ concerted rotation …
where emphasis has been made on the correct representation of the α/γ concerted rotation …
Twenty‐five years of nucleic acid simulations
We present a brief, and largely personal, history of computer simulations of DNA and RNA
oligonucleotides, with an emphasis on duplex structures and the Amber force fields. Both …
oligonucleotides, with an emphasis on duplex structures and the Amber force fields. Both …
[BOOK][B] The mathematics and mechanics of biological growth
A Goriely - 2017 - books.google.com
This monograph presents a general mathematical theory for biological growth. It provides
both a conceptual and a technical foundation for the understanding and analysis of …
both a conceptual and a technical foundation for the understanding and analysis of …
Systematic comparison of the structural and dynamic properties of commonly used water models for molecular dynamics simulations
SP Kadaoluwa Pathirannahalage… - Journal of Chemical …, 2021 - ACS Publications
Water is a unique solvent that is ubiquitous in biology and present in a variety of solutions,
mixtures, and materials settings. It therefore forms the basis for all molecular dynamics …
mixtures, and materials settings. It therefore forms the basis for all molecular dynamics …
Assessing the current state of amber force field modifications for DNA
The utility of molecular dynamics (MD) simulations to model biomolecular structure,
dynamics, and interactions has witnessed enormous advances in recent years due to the …
dynamics, and interactions has witnessed enormous advances in recent years due to the …
[BOOK][B] Nucleic acids in chemistry and biology
GM Blackburn - 2006 - books.google.com
The structure, function and reactions of nucleic acids are central to molecular biology and
are crucial for the understanding of complex biological processes involved. Revised and …
are crucial for the understanding of complex biological processes involved. Revised and …
Conformational analysis of nucleic acids revisited: Curves+
We describe Curves+, a new nucleic acid conformational analysis program which is
applicable to a wide range of nucleic acid structures, including those with up to four strands …
applicable to a wide range of nucleic acid structures, including those with up to four strands …