CHARMM‐GUI DEER facilitator for spin‐pair distance distribution calculations and preparation of restrained‐ensemble molecular dynamics simulations
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DOI: 10.1002/jcc.26032
Abstract: The double electron–electron resonance (DEER) is a powerful structural biology technique to obtain distance information in the range of 18 to 80 å by measuring the dipolar coupling between two unpaired electron spins. The distance distributions… read more here.
Keywords: deer; charmm gui; distance; deer facilitator ... See more keywords
CHARMM‐GUI Enhanced Sampler for various collective variables and enhanced sampling methods
Sign Up to like & getrecommendations! Published in 2022 at "Protein Science"
DOI: 10.1002/pro.4446
Abstract: Enhanced sampling methodologies modifying underlying Hamiltonians can be used for the systems with a rugged potential energy surface that makes it hard to observe convergence using conventional unbiased molecular dynamics (MD) simulations. We present CHARMM‐GUI… read more here.
Keywords: gui enhanced; enhanced sampling; enhanced sampler; charmm gui ... See more keywords
CHARMM-GUI QM/MM Interfacer for a Quantum Mechanical and Molecular Mechanical (QM/MM) Simulation Setup: 1. Semiempirical Methods
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DOI: 10.1021/acs.jctc.4c00439
Abstract: Quantum mechanical (QM) treatments, when combined with molecular mechanical (MM) force fields, can effectively handle enzyme-catalyzed reactions without significantly increasing the computational cost. In this context, we present CHARMM-GUI QM/MM Interfacer, a web-based cyberinfrastructure designed… read more here.
Keywords: charmm gui; gui interfacer; quantum mechanical; semiempirical methods ... See more keywords
CHARMM-GUI EnzyDocker for Protein–Ligand Docking of Multiple Reactive States along a Reaction Coordinate in Enzymes
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DOI: 10.1021/acs.jctc.4c01691
Abstract: Enzymes play crucial roles in all biological systems by catalyzing a myriad of chemical reactions. These reactions range from simple one-step processes to intricate multistep cascades. Predicting mechanistically appropriate binding modes along a reaction pathway… read more here.
Keywords: charmm gui; gui enzydocker; ligand; along reaction ... See more keywords
CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates
Sign Up to like & getrecommendations! Published in 2019 at "Glycobiology"
DOI: 10.1093/glycob/cwz003
Abstract: Characterizing glycans and glycoconjugates in the context of three-dimensional structures is important in understanding their biological roles and developing efficient therapeutic agents. Computational modeling and molecular simulation have become an essential tool complementary to experimental… read more here.
Keywords: modeler; charmm gui; reader modeler; glycan reader ... See more keywords