Molecular dynamics simulation for all
The impact of molecular dynamics (MD) simulations in molecular biology and drug discovery
has expanded dramatically in recent years. These simulations capture the behavior of …
has expanded dramatically in recent years. These simulations capture the behavior of …
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 …
[HTML][HTML] Scalable molecular dynamics on CPU and GPU architectures with NAMD
NAMD is a molecular dynamics program designed for high-performance simulations of very
large biological objects on CPU-and GPU-based architectures. NAMD offers scalable …
large biological objects on CPU-and GPU-based architectures. NAMD offers scalable …
In silico methods and tools for drug discovery
In the past, conventional drug discovery strategies have been successfully employed to
develop new drugs, but the process from lead identification to clinical trials takes more than …
develop new drugs, but the process from lead identification to clinical trials takes more than …
Insights into protein–ligand interactions: mechanisms, models, and methods
X Du, Y Li, YL **a, SM Ai, J Liang, P Sang… - International journal of …, 2016 - mdpi.com
Molecular recognition, which is the process of biological macromolecules interacting with
each other or various small molecules with a high specificity and affinity to form a specific …
each other or various small molecules with a high specificity and affinity to form a specific …
[HTML][HTML] A fast and high-quality charge model for the next generation general AMBER force field
The General AMBER Force Field (GAFF) has been broadly used by researchers all over the
world to perform in silico simulations and modelings on diverse scientific topics, especially in …
world to perform in silico simulations and modelings on diverse scientific topics, especially in …
Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field
Designing tight-binding ligands is a primary objective of small-molecule drug discovery.
Over the past few decades, free-energy calculations have benefited from improved force …
Over the past few decades, free-energy calculations have benefited from improved force …
Relative binding free energy calculations in drug discovery: recent advances and practical considerations
Accurate in silico prediction of protein–ligand binding affinities has been a primary objective
of structure-based drug design for decades due to the putative value it would bring to the …
of structure-based drug design for decades due to the putative value it would bring to the …
Improved peptide and protein torsional energetics with the OPLS-AA force field
The development and validation of new peptide dihedral parameters are reported for the
OPLS-AA force field. High accuracy quantum chemical methods were used to scan φ, ψ, χ1 …
OPLS-AA force field. High accuracy quantum chemical methods were used to scan φ, ψ, χ1 …
Molecular dynamics simulations and drug discovery
This review discusses the many roles atomistic computer simulations of macromolecular (for
example, protein) receptors and their associated small-molecule ligands can play in drug …
example, protein) receptors and their associated small-molecule ligands can play in drug …