Alignment of Flexible Protein Structures. - Maxim Shatsky; Zipora Y. Fligelman; Ruth Nussinov; Haim J. Wolfson (ISMB, 2000)

MultiProt - A Multiple Protein Structural Alignment Algorithm. - Maxim Shatsky; Ruth Nussinov; Haim J. Wolfson (WABI, 2002)

FlexProt: Alignment of Flexible Protein Structures Without a Predefinition of Hinge Regions. - Maxim Shatsky; Ruth Nussinov; Haim J. Wolfson (J. Comput. Biol., 2004)

BioInfo3D: a suite of tools for structural bioinformatics. - Maxim Shatsky; Oranit Dror; Dina Schneidman-Duhovny; Ruth Nussinov; Haim J. Wolfson (Nucleic Acids Res., 2004)

MAPPIS: Multiple 3D Alignment of Protein-Protein Interfaces. - Alexandra Shulman-Peleg; Maxim Shatsky; Ruth Nussinov; Haim J. Wolfson (CompLife, 2005)

Recognition of Binding Patterns Common to a Set of Protein Structures. - Maxim Shatsky; Alexandra Shulman-Peleg; Ruth Nussinov; Haim J. Wolfson (RECOMB, 2005)

The Multiple Common Point Set Problem and Its Application to Molecule Binding Pattern Detection. - Maxim Shatsky; Alexandra Shulman-Peleg; Ruth Nussinov; Haim J. Wolfson (J. Comput. Biol., 2006)

The common point set problem with applications to protein structure analysis - Maxim Shatsky (2006)

EMatch: Discovery of High Resolution Structural Homologues of Protein Domains in Intermediate Resolution Cryo-EM Maps. - Keren Lasker; Oranit Dror; Maxim Shatsky; Ruth Nussinov; Haim J. Wolfson (IEEE ACM Trans. Comput. Biol. Bioinform., 2007)

MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions. - Alexandra Shulman-Peleg; Maxim Shatsky; Ruth Nussinov; Haim J. Wolfson (Nucleic Acids Res., 2008)

Alignment-free local structural search by writhe decomposition. - Degui Zhi; Maxim Shatsky; Steven E. Brenner (Bioinform., 2010)