Metal ion modeling using classical mechanics
P Li, KM Merz Jr - Chemical reviews, 2017 - ACS Publications
Metal ions play significant roles in numerous fields including chemistry, geochemistry,
biochemistry, and materials science. With computational tools increasingly becoming …
biochemistry, and materials science. With computational tools increasingly becoming …
Transport phenomena in nano/molecular confinements
The transport of fluid and ions in nano/molecular confinements is the governing physics of a
myriad of embodiments in nature and technology including human physiology, plants …
myriad of embodiments in nature and technology including human physiology, plants …
[HTML][HTML] Signaling snapshots of a serotonin receptor activated by the prototypical psychedelic LSD
Summary Serotonin (5-hydroxytryptamine [5-HT]) 5-HT2-family receptors represent essential
targets for lysergic acid diethylamide (LSD) and all other psychedelic drugs. Although the …
targets for lysergic acid diethylamide (LSD) and all other psychedelic drugs. Although the …
MCPB. py: A python based metal center parameter builder
P Li, KM Merz Jr - 2016 - ACS Publications
MCPB. py, a python based metal center parameter builder, has been developed to build
force fields for the simulation of metal complexes employing the bonded model approach. It …
force fields for the simulation of metal complexes employing the bonded model approach. It …
Parameterization of monovalent ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB water models
Monovalent ions play significant roles in various biological and material systems. Recently,
four new water models (OPC3, OPC, TIP3P-FB, and TIP4P-FB), with significantly improved …
four new water models (OPC3, OPC, TIP3P-FB, and TIP4P-FB), with significantly improved …
Thyroid Disruption by Bisphenol S Analogues via Thyroid Hormone Receptor β: in Vitro, in Vivo, and Molecular Dynamics Simulation Study
Bisphenol S (4-hydroxyphenyl sulfone, BPS) is increasingly used as a bisphenol A (BPA)
alternative. The global usage of BPS and its analogues (BPSs) resulted in the frequent …
alternative. The global usage of BPS and its analogues (BPSs) resulted in the frequent …
Chalcogen bonding macrocycles and [2] rotaxanes for anion recognition
Electron-deficient heavy chalcogen atoms contain Lewis acidic σ-holes which are able to
form attractive supramolecular interactions, known as chalcogen bonding (ChB), with Lewis …
form attractive supramolecular interactions, known as chalcogen bonding (ChB), with Lewis …
Further along the road less traveled: AMBER ff15ipq, an original protein force field built on a self-consistent physical model
KT Debiec, DS Cerutti, LR Baker… - Journal of chemical …, 2016 - ACS Publications
We present the AMBER ff15ipq force field for proteins, the second-generation force field
developed using the Implicitly Polarized Q (IPolQ) scheme for deriving implicitly polarized …
developed using the Implicitly Polarized Q (IPolQ) scheme for deriving implicitly polarized …
Revised AMBER parameters for bioorganic phosphates
T Steinbrecher, J Latzer, DA Case - Journal of chemical theory …, 2012 - ACS Publications
We report AMBER force field parameters for biological simulations involving
phosphorylation of serine, threonine, or tyrosine. The initial parameters used RESP fitting for …
phosphorylation of serine, threonine, or tyrosine. The initial parameters used RESP fitting for …
Understanding cryptic pocket formation in protein targets by enhanced sampling simulations
Cryptic pockets, that is, sites on protein targets that only become apparent when drugs bind,
provide a promising alternative to classical binding sites for drug development. Here, we …
provide a promising alternative to classical binding sites for drug development. Here, we …