title: Force fields and scoring functions for carbohydrate simulation.
abstract: Carbohydrate dynamics plays a vital role in many biological processes, but we are not currently able to probe this with experimental approaches. The highly flexible nature of carbohydrate structures differs in many aspects from other biomolecules, posing significant challenges for studies employing computational simulation. Over past decades, computational study of carbohydrates has been focused on the development of structure prediction methods, force field optimization, molecular dynamics simulation, and scoring functions for carbohydrate-protein interactions. Advances in carbohydrate force fields and scoring functions can be largely attributed to enhanced computational algorithms, application of quantum mechanics, and the increasing number of experimental structures determined by X-ray and NMR techniques. The conformational analysis of carbohydrates is challengeable and has gone into intensive study in elucidating the anomeric, the exo-anomeric, and the gauche effects. Here, we review the issues associated with carbohydrate force fields and scoring functions, which will have a broad application in the field of carbohydrate-based drug design.
authors.affiliation: Medical College of Nanchang University, 461 Bayi Road, Nanchang, Jiangxi 330066, China; Drug Discovery and Design Center, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
authors.forename: Xiuming
authors.initials: X
authors.lastname: Xiong
authors.affiliation: Drug Discovery and Design Center, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
authors.forename: Zhaoqiang
authors.initials: Z
authors.lastname: Chen
authors.affiliation: UCB Pharma, 216 Bath Road, Slough SL1 4EN, United Kingdom.
authors.forename: Benjamin P
authors.initials: BP
authors.lastname: Cossins
authors.affiliation: Drug Discovery and Design Center, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
authors.forename: Zhijian
authors.initials: Z
authors.lastname: Xu
authors.affiliation: Drug Discovery and Design Center, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Shao
authors.affiliation: Drug Discovery and Design Center, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
authors.forename: Kai
authors.initials: K
authors.lastname: Ding
authors.affiliation: Medical College of Nanchang University, 461 Bayi Road, Nanchang, Jiangxi 330066, China; Drug Discovery and Design Center, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China. Electronic address: wlzhu@mail.shcnc.ac.cn.
authors.forename: Weiliang
authors.initials: W
authors.lastname: Zhu
authors.affiliation: Drug Discovery and Design Center, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; UCB Pharma, 216 Bath Road, Slough SL1 4EN, United Kingdom. Electronic address: Jiye.Shi@ucb.com.
authors.forename: Jiye
authors.initials: J
authors.lastname: Shi
mesh_terms: D000818:Animals; D050260:Carbohydrate Metabolism; D002241:Carbohydrates / Q000737:chemistry*; D006801:Humans; D006860:Hydrogen Bonding; D008958:Models, Molecular; D011506:Proteins / Q000378:metabolism; D013816:Thermodynamics
chemical_list: D002241:Carbohydrates; D011506:Proteins
keywords: Carbohydrate force field; Carbohydrate–protein interaction; Drug design; Scoring function; Simulation