Mesh Generation and Flexible Shape Comparisons for Bio-Molecules

Abstract

Novel approaches for generating and comparing flexible (non-rigid) molecular surface meshes are developed. The mesh-generating method is fast and memory-efficient. The resulting meshes are smooth and accurate, and possess high mesh quality. An isometric-invariant shape descriptor based on the Laplace- Beltrami operator is then explored for mesh comparing. The new shape descriptor is more powerful in discriminating different surface shapes but rely only on a small set of signature values. The shape descriptor is applied to shape comparison between molecules with deformed structures. The proposed methods are implemented into a program that can be used as a stand-alone software tool or as a plug-in to other existing molecular modeling tools. Particularly, the code is encapsulated into a software toolkit with a user-friendly graphical interface developed by the authors.

PLO3S: Protein LOcal Surficial Similarity Screening

“…Proteins sharing a related function display similar surfaces that can be independent of their sequence and/or structure similarity [44] , [18] , [27] . Different methods based on protein surface comparison have been developed for protein-protein interactions prediction [45] , [39] , [12] , protein structural alignment [29] or protein shapes classification [18] , [15] , [43] , [28] , [9] , [14] , [27] , [32] .…”

PLO3S : Protein LOcal Surficial Similarity Screening

“…Proteins sharing a related function display similar surfaces that can be independent of their sequence and/or structure similarity [15, 23, 39]. Different methods based on protein surface comparison have been developed for protein-protein interactions prediction [11, 34, 40], protein structural alignment [25] or protein shapes classification [8, 12, 13, 15, 23, 24, 27, 38].…”

Comparative evaluation of shape retrieval methods on macromolecular surfaces: an application of computer vision methods in structural bioinformatics

“…Functionally related proteins often share similar molecular surface properties despite a potentially low sequence and/or backbone conformation similarity ( Han et al , 2019 ; Sael et al , 2008a ). Different categories of methods based on protein surface shape have been developed over time such as protein–protein docking ( Ruiz Echartea et al , 2019 ; Schneidman-Duhovny et al , 2005 ), protein structure alignment ( Mavridis and Ritchie, 2010 ) or protein surface shape comparison methods ( Craciun et al , 2017 ; Gainza et al , 2020 ; Gao et al , 2016 ; Gramada and Bourne, 2006 ; Guzenko et al , 2020 ; Han et al , 2019 ; Mak et al , 2008 ; Sael et al , 2008b ). Shape comparison and retrieval methods have been extensively developed in the computer vision field, notably for military, civil security or medical imaging applications ( Bustos et al , 2007 ).…”