Parallelized multiple alignment. - Jens Kleinjung; Nigel Douglas; Jaap Heringa (Bioinform., 2002)

Testing homology with Contact Accepted mutatiOn (CAO): a contact-based Markov model of protein evolution. - Kuang Lin; Jens Kleinjung; William R. Taylor; Jaap Heringa (Comput. Biol. Chem., 2003)

POPS: a fast algorithm for solvent accessible surface areas at atomic and residue level. - Luigi Cavallo; Jens Kleinjung; Franca Fraternali (Nucleic Acids Res., 2003)

POPSCOMP: an automated interaction analysis of biomolecular complexes. - Jens Kleinjung; Franca Fraternali (Nucleic Acids Res., 2005)

MinSet: a general approach to derive maximally representative database subsets by using fragment dictionaries and its application to the SCOP database. - Alessandro Pandini; Laura Bonati; Franca Fraternali; Jens Kleinjung (Bioinform., 2007)

Structural alphabets derived from attractors in conformational space. - Alessandro Pandini; Arianna Fornili; Jens Kleinjung (BMC Bioinform., 2010)

STRIKE: evaluation of protein MSAs using a single 3D structure. - Carsten Kemena; Jean-François Taly; Jens Kleinjung; Cédric Notredame (Bioinform., 2011)

GSATools: analysis of allosteric communication and functional local motions using a structural alphabet. - Alessandro Pandini; Arianna Fornili; Franca Fraternali; Jens Kleinjung (Bioinform., 2013)