Local elevation: A method for improving the searching properties of molecular dynamics simulation. - Thomas Huber; Andrew Ernest Torda; Wilfred F. van Gunsteren (J. Comput. Aided Mol. Des., 1994)

Algorithms for Clustering Molecular Dynamics Confogurations. - Andrew Ernest Torda; Wilfred F. van Gunsteren (J. Comput. Chem., 1994)

Sausage: protein threading with flexible force fields. - Thomas Huber; Anthony J. Russell; Daniel Ayers; Andrew Ernest Torda (Bioinform., 1999)

Protein sequence threading, the alignment problem, and a two-step strategy. - Thomas Huber; Andrew Ernest Torda (J. Comput. Chem., 1999)

Amino acid similarity matrices based on force fields. - Zsuzsanna Dosztányi; Andrew Ernest Torda (Bioinform., 2001)

Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices. - Andrew Ernest Torda; James B. Procter; Thomas Huber (Nucleic Acids Res., 2004)

Editorial. - Andrew Ernest Torda; Thomas Lengauer (Bioinform., 2006)

Protein sequence and structure alignments within one framework. - Gundolf Schenk; Thomas Margraf; Andrew Ernest Torda (Algorithms Mol. Biol., 2008)

The SALAMI protein structure search server. - Thomas Margraf; Gundolf Schenk; Andrew Ernest Torda (Nucleic Acids Res., 2009)

RNA secondary structure prediction using a self-consistent mean field approach. - Jens Kleesiek; Andrew Ernest Torda (J. Comput. Chem., 2010)

RNA secondary structure diagrams for very large molecules: RNAfdl. - Nikolai Hecker; Tim Wiegels; Andrew Ernest Torda (Bioinform., 2013)

Fast alignment and comparison of RNA structures. - Tim Wiegels; Stefan Bienert; Andrew Ernest Torda (Bioinform., 2013)

Modifications to glucose-6-phosphate dehydrogenase for industrial applications: predictions and tests. - Martin Mosisch; Jan Simons; Lutz Hilterhaus; Andrew Ernest Torda (J. Cheminformatics, 2013)

Not assessing the efficiency of multiple sequence alignment programs. - Andrew Ernest Torda (Algorithms Mol. Biol., 2014)

The LUX Score: A Metric for Lipidome Homology. - Chakravarthy Marella; Andrew Ernest Torda; Dominik Schwudke (PLoS Comput. Biol., 2015)

Lipidome visualisation, comparison, and analysis in a vector space. - Timur Olzhabaev; Lukas Müller; Daniel Krause 005; Dominik Schwudke; Andrew Ernest Torda (PLoS Comput. Biol., 2025)