Bioinformatik interaktiv - Algorithmen und Praxis. - Rainer Merkl; Stephan Waack (Wiley-VCH, 2003)

YACOP: Enhanced gene prediction obtained by a combination of existing methods. - Maike Tech; Rainer Merkl (Silico Biol., 2003)

secureBLAST. - Arnim Wiezer; Rainer Merkl (Silico Biol., 2003)

Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites. - Peter Meinicke; Maike Tech; Burkhard Morgenstern; Rainer Merkl (BMC Bioinform., 2004)

SIGI: score-based identification of genomic islands. - Rainer Merkl (BMC Bioinform., 2004)

Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. - Stephan Waack; Oliver Keller; Roman Asper; Thomas Brodag; Carsten Damm; Wolfgang Florian Fricke; Katharina Surovcik; Peter Meinicke; Rainer Merkl (BMC Bioinform., 2006)

AMIGOS: A Method for the Inspection of Genomic Organisation or Structure and its Application to Characterise Conserved Gene Arrangements. - Rainer Merkl (Silico Biol., 2006)

H2r: Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments. - Rainer Merkl; Matthias Zwick (BMC Bioinform., 2008)

TransCent: Computational enzyme design by transferring active sites and considering constraints relevant for catalysis. - André Fischer; Nils Enkler; Gerd Neudert; Marco Bocola; Reinhard Sterner; Rainer Merkl (BMC Bioinform., 2009)

PROCOS: Computational analysis of protein-protein complexes. - Florian Fink; Jochen Hochrein; Vincent Wolowski; Rainer Merkl; Wolfram Gronwald (J. Comput. Chem., 2011)

Key2Ann: a tool to process sequence sets by replacing database identifiers with a human-readable annotation. - Andreas Pürzer; Felix Grassmann; Dietmar Birzer; Rainer Merkl (J. Integr. Bioinform., 2011)

CLIPS-1D: analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure. - Jan-Oliver Janda; Markus Busch; Fabian Kück; Mikhail Porfenenko; Rainer Merkl (BMC Bioinform., 2012)

CLIPS-4D: a classifier that distinguishes structurally and functionally important residue-positions based on sequence and 3D data. - Jan-Oliver Janda; Andreas Meier 007; Rainer Merkl (Bioinform., 2013)

H2rs: Deducing evolutionary and functionally important residue positions by means of an entropy and similarity based analysis of multiple sequence alignments. - Jan-Oliver Janda; Ajmal Popal; Jochen Bauer; Markus Busch; Michael Klocke; Wolfgang Spitzer; Jörg Keller 001; Rainer Merkl (BMC Bioinform., 2014)

An assessment of catalytic residue 3D ensembles for the prediction of enzyme function. - Clemens Zvácek; Gerald Friedrichs; Leonhard Heizinger; Rainer Merkl (BMC Bioinform., 2015)

AGeNNT: annotation of enzyme families by means of refined neighborhood networks. - Florian Kandlinger; Maximilian G. Plach; Rainer Merkl (BMC Bioinform., 2017)

Rosetta: MSF: a modular framework for multi-state computational protein design. - Patrick Löffler; Samuel Schmitz; Enrico Hupfeld; Reinhard Sterner; Rainer Merkl (PLoS Comput. Biol., 2017)

Conserved genomic neighborhood is a strong but no perfect indicator for a direct interaction of microbial gene products. - Robert Esch; Rainer Merkl (BMC Bioinform., 2020)

Rosetta design with co-evolutionary information retains protein function. - Samuel Schmitz; Moritz Ertelt; Rainer Merkl; Jens Meiler (PLoS Comput. Biol., 2021)