Chemistry, structure and function of approved oligonucleotide therapeutics
M Egli, M Manoharan - Nucleic Acids Research, 2023 - academic.oup.com
Eighteen nucleic acid therapeutics have been approved for treatment of various diseases in
the last 25 years. Their modes of action include antisense oligonucleotides (ASOs), splice …
the last 25 years. Their modes of action include antisense oligonucleotides (ASOs), splice …
Machine learning methods for small data challenges in molecular science
Small data are often used in scientific and engineering research due to the presence of
various constraints, such as time, cost, ethics, privacy, security, and technical limitations in …
various constraints, such as time, cost, ethics, privacy, security, and technical limitations in …
LAMMPS-a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales
Since the classical molecular dynamics simulator LAMMPS was released as an open source
code in 2004, it has become a widely-used tool for particle-based modeling of materials at …
code in 2004, it has become a widely-used tool for particle-based modeling of materials at …
gmx_MMPBSA: a new tool to perform end-state free energy calculations with GROMACS
MS Valdés-Tresanco… - Journal of chemical …, 2021 - ACS Publications
Molecular mechanics/Poisson–Boltzmann (Generalized-Born) surface area is one of the
most popular methods to estimate binding free energies. This method has been proven to …
most popular methods to estimate binding free energies. This method has been proven to …
A universal graph deep learning interatomic potential for the periodic table
Interatomic potentials (IAPs), which describe the potential energy surface of atoms, are a
fundamental input for atomistic simulations. However, existing IAPs are either fitted to narrow …
fundamental input for atomistic simulations. However, existing IAPs are either fitted to narrow …
[HTML][HTML] GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
GROMACS is one of the most widely used open-source and free software codes in
chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of …
chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of …
ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB
JA Maier, C Martinez, K Kasavajhala… - Journal of chemical …, 2015 - ACS Publications
Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force
field is required. The Amber ff99SB force field improved protein secondary structure balance …
field is required. The Amber ff99SB force field improved protein secondary structure balance …
End-point binding free energy calculation with MM/PBSA and MM/GBSA: strategies and applications in drug design
Molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) and molecular
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …
Current trends in computer aided drug design and a highlight of drugs discovered via computational techniques: A review
Computer-aided drug design (CADD) is one of the pivotal approaches to contemporary pre-
clinical drug discovery, and various computational techniques and software programs are …
clinical drug discovery, and various computational techniques and software programs are …
The halogen bond
The halogen bond occurs when there is evidence of a net attractive interaction between an
electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic …
electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic …