title: 3DMolNavi: a web-based retrieval and navigation tool for flexible molecular shape comparison.
abstract: BACKGROUND
  Many molecules of interest are flexible and undergo significant shape deformation as part of their function, but most existing methods of molecular shape comparison treat them as rigid shapes, which may lead to incorrect measure of the shape similarity of flexible molecules. Currently, there still is a limited effort in retrieval and navigation for flexible molecular shape comparison, which would improve data retrieval by helping users locate the desirable molecule in a convenient way.
  
  
  RESULTS
  To address this issue, we develop a web-based retrieval and navigation tool, named 3DMolNavi, for flexible molecular shape comparison. This tool is based on the histogram of Inner Distance Shape Signature (IDSS) for fast retrieving molecules that are similar to a query molecule, and uses dimensionality reduction to navigate the retrieved results in 2D and 3D spaces. We tested 3DMolNavi in the Database of Macromolecular Movements (MolMovDB) and CATH. Compared to other shape descriptors, it achieves good performance and retrieval results for different classes of flexible molecules.
  
  
  CONCLUSIONS
  The advantages of 3DMolNavi, over other existing softwares, are to integrate retrieval for flexible molecular shape comparison and enhance navigation for user's interaction. 3DMolNavi can be accessed via https://engineering.purdue.edu/PRECISE/3dmolnavi/index.html.
authors.affiliation: School of Software, Tsinghua University, Beijing 100084, China. liuyushen@tsinghua.edu.cn
authors.forename: Yu-Shen
authors.initials: YS
authors.lastname: Liu
authors.forename: Meng
authors.initials: M
authors.lastname: Wang
authors.forename: Jean-Claude
authors.initials: JC
authors.lastname: Paul
authors.forename: Karthik
authors.initials: K
authors.lastname: Ramani
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D008968:Molecular Conformation; D012984:Software; D014584:User-Computer Interface