title: MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature.
abstract: BACKGROUND
  Aligning similar molecular structures is an important step in the process of bio-molecular structure and function analysis. Molecular surfaces are simple representations of molecular structure that are easily constructed from various forms of molecular data such as 3D atomic coordinates (PDB) and Electron Microscopy (EM) data.
  
  
  METHODS
  We present a Multi-Scale Morse-Smale Molecular-Surface Alignment tool, MS3ALIGN, which aligns molecular surfaces based on significant protrusions on the molecular surface. The input is a pair of molecular surfaces represented as triangle meshes. A key advantage of MS3ALIGN is computational efficiency that is achieved because it processes only a few carefully chosen protrusions on the molecular surface. Furthermore, the alignments are partial in nature and therefore allows for inexact surfaces to be aligned.
  
  
  RESULTS
  The method is evaluated in four settings. First, we establish performance using known alignments with varying overlap and noise values. Second, we compare the method with SurfComp, an existing surface alignment method. We show that we are able to determine alignments reported by SurfComp, as well as report relevant alignments not found by SurfComp. Third, we validate the ability of MS3ALIGN to determine alignments in the case of structurally dissimilar binding sites. Fourth, we demonstrate the ability of MS3ALIGN to align iso-surfaces derived from cryo-electron microscopy scans.
  
  
  CONCLUSIONS
  We have presented an algorithm that aligns Molecular Surfaces based on the topology of surface curvature. A webserver and standalone software implementation of the algorithm available at http://vgl.serc.iisc.ernet.in/ms3align.
authors.affiliation: Department of Computer Science and Automation, Indian Institute of Science, Bangalore, 560012, India. nithin@csa.iisc.ernet.in.
authors.forename: Nithin
authors.initials: N
authors.lastname: Shivashankar
authors.affiliation: Department of Computer Science and Automation, Indian Institute of Science, Bangalore, 560012, India.
authors.forename: Sonali
authors.initials: S
authors.lastname: Patil
authors.affiliation: Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India.
authors.forename: Amrisha
authors.initials: A
authors.lastname: Bhosle
authors.affiliation: Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India.
authors.forename: Nagasuma
authors.initials: N
authors.lastname: Chandra
authors.affiliation: Department of Computer Science and Automation, and Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, 560012, India. vijayn@csa.iisc.ernet.in.
authors.forename: Vijay
authors.initials: V
authors.lastname: Natarajan
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D019295:Computational Biology; D003198:Computer Simulation; D008958:Models, Molecular; D015394:Molecular Structure; D016415:Sequence Alignment; D012984:Software