The SAMPL2 blind prediction challenge: introduction and overview

MT Geballe, AG Skillman, A Nicholls, JP Guthrie… - Journal of computer …, 2010 - Springer
The interactions between a molecule and the aqueous environment underpin any process
that occurs in solution, from simple chemical reactions to protein–ligand binding to protein …

Subunit-specific agonist activity at NR2A-, NR2B-, NR2C-, and NR2D-containing N-methyl-D-aspartate glutamate receptors

K Erreger, MT Geballe, A Kristensen, PE Chen… - Molecular …, 2007 - ASPET
The four N-methyl-d-aspartate (NMDA) receptor NR2 subunits (NR2A-D) have different
developmental, anatomical, and functional profiles that allow them to serve different roles in …

Structural features of the glutamate binding site in recombinant NR1/NR2A N-methyl-D-aspartate receptors determined by site-directed mutagenesis and molecular …

PE Chen, MT Geballe, PJ Stansfeld, AR Johnston… - Molecular …, 2005 - ASPET
We have used site-directed mutagenesis of amino acids located within the S1 and S2 ligand
binding domains of the NR2A N-methyl-d-aspartate (NMDA) receptor subunit to explore the …

Blind prediction of host–guest binding affinities: a new SAMPL3 challenge

…, AR Urbach, L Isaacs, MT Geballe… - Journal of computer …, 2012 - Springer
The computational prediction of protein–ligand binding affinities is of central interest in early-stage
drug-discovery, and there is a widely recognized need for improved methods. Low …

Modulation of glycine potency in rat recombinant NMDA receptors containing chimeric NR2A/2D subunits expressed in Xenopus laevis oocytes

PE Chen, MT Geballe, E Katz, K Erreger… - The Journal of …, 2008 - Wiley Online Library
Heteromeric NMDARs are composed of coagonist glycine‐binding NR1 subunits and
glutamate‐binding NR2 subunits. The majority of functional NMDARs in the mammalian central …

Structural determinants of D-cycloserine efficacy at the NR1/NR2C NMDA receptors

…, PB Burger, A Prakash, MT Geballe… - Journal of …, 2010 - Soc Neuroscience
We have studied relative efficacies of NR1 agonists glycine and d-cycloserine (DCS), and
found efficacy to be dependent on the NR2 subunit. DCS shows partial agonism at NR1/NR2B …

The SAMPL3 blind prediction challenge: transfer energy overview

MT Geballe, JP Guthrie - Journal of Computer-Aided Molecular Design, 2012 - Springer
Prediction of the free energy of solvation of a small molecule, or its transfer energy, is a
necessary step along the path towards calculating the interactions between molecules that occur …

Mechanism of partial agonism at NMDA receptors for a conformationally restricted glutamate analog

K Erreger, MT Geballe, SM Dravid… - Journal of …, 2005 - Soc Neuroscience
The NMDA ionotropic glutamate receptor is ubiquitous in mammalian central neurons.
Because partial agonists bind to the same site as glutamate but induce less channel activation, …

[HTML][HTML] The serine protease plasmin cleaves the amino-terminal domain of the NR2A subunit to relieve zinc inhibition of the N-methyl-D-aspartate receptors

H Yuan, KM Vance, CE Junge, MT Geballe… - Journal of biological …, 2009 - ASBMB
Zinc is hypothesized to be co-released with glutamate at synapses of the central nervous
system. Zinc binds to NR1/NR2A N-methyl-d-aspartate (NMDA) receptors with high affinity and …

SiteHopper-a unique tool for binding site comparison

…, PCD Hawkins, R Tolbert, MT Geballe - Journal of Cheminformatics, 2014 - Springer
Knowledge of and information about protein binding sites has become increasingly important
in the drug discovery process and not just for molecular biologists [1]. By comparing …