Literature DB >> 25753723

Molecular dynamics simulations of glycoproteins using CHARMM.

Sairam S Mallajosyula1, Sunhwan Jo, Wonpil Im, Alexander D MacKerell.   

Abstract

Molecular dynamics simulations are an effective tool to study the structure, dynamics, and thermodynamics of carbohydrates and proteins. However, the simulations of heterogeneous glycoprotein systems have been limited due to the lack of appropriate molecular force field parameters describing the linkage between the carbohydrate and the protein regions as well as the tools to prepare these systems for modeling studies. In this work we outline the recent developments in the CHARMM carbohydrate force field to treat glycoproteins and describe in detail the step-by-step procedures involved in building glycoprotein geometries using CHARMM-GUI Glycan Reader.

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Year:  2015        PMID： 25753723      PMCID： PMC4537648          DOI： 10.1007/978-1-4939-2343-4_25

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  53 in total

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2.  CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling.

Authors:  Olgun Guvench; Sairam S Mallajosyula; E Prabhu Raman; Elizabeth Hatcher; Kenno Vanommeslaeghe; Theresa J Foster; Francis W Jamison; Alexander D Mackerell
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4.  CHARMM-GUI: a web-based graphical user interface for CHARMM.

Authors:  Sunhwan Jo; Taehoon Kim; Vidyashankara G Iyer; Wonpil Im
Journal:  J Comput Chem       Date:  2008-08       Impact factor: 3.376

Review 5.  CHARMM: the biomolecular simulation program.

Authors:  B R Brooks; C L Brooks; A D Mackerell; L Nilsson; R J Petrella; B Roux; Y Won; G Archontis; C Bartels; S Boresch; A Caflisch; L Caves; Q Cui; A R Dinner; M Feig; S Fischer; J Gao; M Hodoscek; W Im; K Kuczera; T Lazaridis; J Ma; V Ovchinnikov; E Paci; R W Pastor; C B Post; J Z Pu; M Schaefer; B Tidor; R M Venable; H L Woodcock; X Wu; W Yang; D M York; M Karplus
Journal:  J Comput Chem       Date:  2009-07-30       Impact factor: 3.376

6.  A new GROMOS force field for hexopyranose-based carbohydrates.

Authors:  Roberto D Lins; Philippe H Hünenberger
Journal:  J Comput Chem       Date:  2005-10       Impact factor: 3.376

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Authors:  Xiao Zhu; Pedro E M Lopes; Alexander D Mackerell
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Authors:  Olgun Guvench; Shannon N Greene; Ganesh Kamath; John W Brady; Richard M Venable; Richard W Pastor; Alexander D Mackerell
Journal:  J Comput Chem       Date:  2008-11-30       Impact factor: 3.376

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Authors:  E Cristina Stanca-Kaposta; David P Gamblin; Emilio J Cocinero; Jann Frey; Romano T Kroemer; Antony J Fairbanks; Benjamin G Davis; John P Simons
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10.  Glycoconjugate Data Bank: Structures--an annotated glycan structure database and N-glycan primary structure verification service.

Authors:  Taku Nakahara; Ryo Hashimoto; Hiroaki Nakagawa; Kenji Monde; Nobuaki Miura; Shin-Ichiro Nishimura
Journal:  Nucleic Acids Res       Date:  2007-10-11       Impact factor: 16.971
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6.  Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2.

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