Incorporation of Carbohydrates into Macromolecular Force Fields: Development and Validation

Tschampel, Sarah M.; Woods, Robert J.

doi:10.1021/bk-2006-0930.ch013

Cited by 13 publications

(8 citation statements)

References 77 publications

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“…4) in hexopyranoses. In fact, the weakening of 1–4 interactions (O6–O5), relative to 1–5 (O6–O4), prevents the accurate fitting of the rotational properties for this linkage [78,90]. Conversely, choosing not to use 1–4 scaling factors may cause a conflict with the treatment of non-bonded interactions in protein force fields.…”

Section: Carbohydrate Force Fieldsmentioning

confidence: 99%

“…Various parameterization protocols have been developed to generate force field terms specific to carbohydrates [91]. Each of these protocols results in a unique parameter set, with characteristic strengths and weaknesses not only in terms of performance but also in terms of ease of implementation, transferability or generality for extension to glycans outside of the original parameterization scheme or to glycomimetics, as well as compatibility with other biomolecules and solvent models [29,69].…”

Section: Carbohydrate Force Fieldsmentioning

confidence: 99%

“…Several reviews of earlier developments of carbohydrate force fields are available in the literature [76,90,92–95]. In the next sections, we discuss the most recent developments of widely used carbohydrate force fields (i.e.…”

Section: Carbohydrate Force Fieldsmentioning

confidence: 99%

See 2 more Smart Citations

Molecular simulations of carbohydrates and protein–carbohydrate interactions: motivation, issues and prospects

Fadda

Woods

2010

Drug Discovery Today

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172

122

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The characterization of the 3D structure of oligosaccharides, their conjugates and analogs is particularly challenging for traditional experimental methods. Molecular simulation methods provide a basis for interpreting sparse experimental data and for independently predicting conformational and dynamic properties of glycans. Here, we summarize and analyze the issues associated with modeling carbohydrates, with a detailed discussion of four of the most recently developed carbohydrate force fields, reviewed in terms of applicability to natural glycans, carbohydrate–protein complexes and the emerging area of glycomimetic drugs. In addition, we discuss prospectives and new applications of carbohydrate modeling in drug discovery.

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Section: Carbohydrate Force Fieldsmentioning

confidence: 99%

Section: Carbohydrate Force Fieldsmentioning

confidence: 99%

See 1 more Smart Citation

Molecular simulations of carbohydrates and protein–carbohydrate interactions: motivation, issues and prospects

Fadda

Woods

2010

Drug Discovery Today

Self Cite

172

122

View full text Add to dashboard Cite

show abstract

“…A reoptimization of the torsional parameters used in GROMOS GROMOS 45A4 for the x dihedral angle (at least in hexopyranoses with an axial 4-OH group) seems therefore to be required (work in progress). For comparison, the population ratios g + /t/g À for Glc and Gal obtained with other commonly used force fields (see also 98,272 …”

Section: Conformation Of the Exocyclic Dihedral Anglesmentioning

confidence: 99%

“…267,268 For completeness, it should be mentioned that ab initio MD simulations of carbohydrates have also been performed. 98,269,270 The most commonly used force fields have been discussed in recent reviews, 217,219,271,272 and a number of more or less extensive force field comparisons (against vacuum, 233,273,274 solid state 275,276 or solution 273,277,278 data) have also been undertaken.…”

Section: Introductionmentioning

confidence: 99%