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Comparison of multiple Amber force fields and development of improved protein backbone parameters
The ff94 force field that is commonly associated with the Amber simulation package is one of the most widely used parameter sets for biomolecular simulation. After a decade of extensive use andExpand
Crystallographic structure of the K intermediate of bacteriorhodopsin: conservation of free energy after photoisomerization of the retinal.
The K state, an early intermediate of the bacteriorhodopsin photocycle, contains the excess free energy used for light-driven proton transport. The energy gain must reside in or near theExpand
HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations.
We report unrestrained, all-atom molecular dynamics simulations of HIV-1 protease that sample large conformational changes of the active site flaps. In particular, the unliganded protease undergoesExpand
Comparison of class A and D G protein-coupled receptors: common features in structure and activation.
All G protein-coupled receptors (GPCRs) share a common seven TM helix architecture and the ability to activate heterotrimeric G proteins. Nevertheless, these receptors have widely divergent sequencesExpand
Helix Movement is Coupled to Displacement of the Second Extracellular Loop in Rhodopsin Activation
The second extracellular loop (EL2) of rhodopsin forms a cap over the binding site of its photoreactive 11-cis retinylidene chromophore. A crucial question has been whether EL2 forms a reversibleExpand
Location of Trp265 in metarhodopsin II: implications for the activation mechanism of the visual receptor rhodopsin.
Isomerization of the 11-cis retinal chromophore in the visual pigment rhodopsin is coupled to motion of transmembrane helix H6 and receptor activation. We present solid-state magic angle spinning NMRExpand
Location of the Retinal Chromophore in the Activated State of Rhodopsin*
Rhodopsin is a highly specialized G protein-coupled receptor (GPCR) that is activated by the rapid photochemical isomerization of its covalently bound 11-cis-retinal chromophore. UsingExpand
Improving Convergence of Replica-Exchange Simulations through Coupling to a High-Temperature Structure Reservoir.
TLDR
We propose a new variant to REMD where the replicas are also permitted to exchange with an ensemble of structures that have been generated in advance using high-temperature MD simulations, similar in spirit to J-walking methods. Expand
Structure-Kinetic Relationships of Passive Membrane Permeation from Multiscale Modeling.
Passive membrane permeation of small molecules is essential to achieve the required absorption, distribution, metabolism, and excretion (ADME) profiles of drug candidates, in particular intestinalExpand
Hidden bias in the DUD-E dataset leads to misleading performance of deep learning in structure-based virtual screening
TLDR
Hidden bias in the DUD-E dataset leads to misleading performance of deep learning in structure-based virtual screening. Expand
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