Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years seve...

To gain a better understanding of how monovalent salt under physiological conditions affects plasma membranes, we have performed 200 ns atomic-scale molecular dynamics simulations of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) lipid bilayers. These two systems provide representative models for the outer and inner leaflets of the plasma membrane, respectively. The implications of ...

Software engineering is a mature industry of human activity focused on the creation, deployment, marketing and maintenance software. The fundamental concepts are life cycle model; three main components phases - products, processes resources; methodologies for creating, deployment maintaining foun- dation technological advances that lead to new high performance products. As functionality product...

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Abstract Molecular docking is one of the most popular computational tools for hit discovery step in drug design. However, there ample room improvement docking's ability to identify correct binding modes and discriminate active from decoy compounds. dynamics (MD) simulations protein–ligand structures have been shown be effective improving results. Here, we present CHARMM‐GUI high‐throughput simu...