Description ParmEd is a package designed to facilitate creating and easily manipulatingmolecular systems that are fully described by a common classical force field.Supported force fields include Amber, CHARMM, AMOEBA, and several others thatshare a similar functional form (e.g., GROMOS). ParmE ...
HCS Chan, D McCarthy, J Li, K Palczewski, S Yuan *. Trends in Pharmacological Science (2017) DOI: http://dx.doi.org/10.1016/j.tips.2017.08.004 Pain is both a major clinical and economic problem, affecting more people than diabetes, heart disease, and cancer combined. While a ...
CHARMM36m: An Improved Force Field for Folded and Intrinsically Disordered Proteins. Nature Methods, 2017 Jan; 14(1): 71–73. doi: 10.1038/nmeth.4067 Disordered protein is a challenge for molecular dynamic simulations, especially considering the lack of a proper force field. In a rece ...
Description - Chemical interactions, lateral heterogeneity, and the lipid zoo. Lipidomic studies of membranes reveal a huge diversity of lipid types, the composition of which varies with cell and membrane type. All-atom models have recently been shown to quantitatively capture the chemistry of ...
Yuan, S*, Peng, Q, Palczewski, K., Vogel, H, Filipek, S*. (2016) Mechanistic Studies on the Stereoselectivity of the Serotonin 5-HT1A Receptor. Angew. Chem. Int. Ed DOI: 10.1002/anie.201603766R1 (2016) Full Text G-protein-coupled receptors (GPCRs) are involved in a wide range ...
As the most widely used docking tool, Autodock team released next version: AutodockFR. AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility, Pradeep Anand Ravindranath, Stefano Forli, David S. Goodsell, Arthur J. Olson, Michel F. Sanner PLOS ...
Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser Nature (2015) doi:10.1038/nature14656 full text PDB: 4ZWJ Abstract: G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction a ...
All protein ligand interactions take place in bulk environment. It is important to predict how water molecules in the binding pocket affect their interactions. Thus, a number of tools, including WATsite , Waterdock , Schrodinger Watermap , OpenEYE SZMAP and WaterLap , were developed for this ...
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