Summary: Amino acid residues showing above background levels of conservation are often indicative of functionally significant regions within a protein. Understanding how the sequence conservation profile relates in space requires projection onto a protein structure, a potentially time-consuming process. 3DPatch is a web application that streamlines this task by automatically generating multiple sequence alignments (where appropriate) and finding structural homologs, presenting the user with a choice of structures matching their query, annotated with residue conservation scores in a matter of seconds. Availability and implementation: 3DPatch is written in JavaScript and is freely available at http://www.skylign.org/3DPatch/. Mozilla Firefox, Google Chrome, and Safari web browsers are supported. Source code is available under MIT license at https://github.com/davidjakubec/3DPatch. Supplementary information: Supplementary data are available at Bioinformatics online.

Department of Bioinformatics Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague 6 166 10 Czech Republic

Department of Bioinformatics Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague 6 166 10 Czech Republic Department of Physical and Macromolecular Chemistry Faculty of Science Charles University Prague 2 128 43 Czech Republic

European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge UK

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