Journal ArticleDOI
Investigation on the binding specificity of Agrocybe cylindracea galectin towards α(2,6)-linked sialyllactose by molecular modeling and molecular dynamics simulations
Ponnusamy Parasuraman,Jeyasigamani F. A. Selvin,M. Michael Gromiha,Kazuhiko Fukui,K. Veluraja +4 more
TLDR
Analysis of the interaction patterns of the carbohydrate at the binding site of wild type and mutated lectins revealed that sialic acid contributed more to the binding when compared with other sugar units in the trisaccharide and enhanced the binding specificity of ACG towards α(2,6)-linked sialyllactose.About:
This article is published in Journal of Carbohydrate Chemistry.The article was published on 2019-07-09. It has received 1 citations till now. The article focuses on the topics: Galectin.read more
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Structural and conformational dynamics of human milk oligosaccharides, lacto-N-fucopentaose I and II, through molecular dynamics simulation
TL;DR: In this article , the structural flexibility of glycosidic linkage and intramolecular interactions between molecules was investigated for human breast milk oligosaccharide (HMOs), lacto-N-fucopentaose (LNFP) I and II, investigated through MD simulation for 250 ns, and its replicate.
References
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Scalable molecular dynamics with NAMD
James C. Phillips,Rosemary Braun,Wei Wang,James C. Gumbart,Emad Tajkhorshid,Elizabeth Villa,Christophe Chipot,Robert D. Skeel,Laxmikant V. Kale,Klaus Schulten +9 more
TL;DR: NAMD as discussed by the authors is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems that scales to hundreds of processors on high-end parallel platforms, as well as tens of processors in low-cost commodity clusters, and also runs on individual desktop and laptop computers.
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MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures
TL;DR: The MOLSCRIPT program as discussed by the authors produces plots of protein structures using several different kinds of representations, including simple wire models, ball-and-stick models, CPK models and text labels.
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Development and testing of a general amber force field.
TL;DR: A general Amber force field for organic molecules is described, designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens.
Journal ArticleDOI
MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.
Bill R. Miller,T. Dwight McGee,Jason M. Swails,Nadine Homeyer,Holger Gohlke,Adrian E. Roitberg +5 more
TL;DR: MMPBSA.py is a program written in Python for streamlining end-state free energy calculations using ensembles derived from molecular dynamics or Monte Carlo simulations, including the Poisson-Boltzmann Model and several implicit solvation models.