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Updated: Feb 10, 2026

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
Published on: July 2, 2010
Molecular modeling of neurological membrane proteins - from binding sites to synapses
Lucy Kate Ladefoged1, Talia Zeppelin1, Birgit Schiøtt1
1Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark.
Abstract:
The field of molecular mechanics studies of proteins has developed enormously since its origin in the 1970's, and many applications and methodologies have branched from the original idea of the force field. The applications of such methodologies are far spread and commonplace in neuroscience research today. In this mini-review, we outline the main methodologies applied when studying events ranging from ligands binding within small binding sites, through overall large-scale conformational changes, to the even larger-scale oligomerization events of neurological membrane proteins. The limitations and caveats of the methods are discussed, while examples of recent applications are described and their implications discussed. We have chosen to focus on the monoamine transporters throughout, with a few examples from neurological membrane proteins such as ionotropic and metabotropic neurotransmitter receptors.
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