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While tools to analyze residue-specific charge distribution of proteins at a given pH exist, currently no tool is available to investigate noncovalent bond changes at two different pH values. To make protein pH sensitivity analysis more accessible, we developed patcHwork, a web server that combines the identification of amino acids undergoing a charge shift with the determination of affected noncovalent bonds at two user-defined pH values. At the sequence-only level, patcHwork applies the Henderson\u2013Hasselbalch equation to determine pH-sensitive residues. When the 3D protein structure is available, patcHwork can be employed to gain mechanistic understanding of the effect of pH. This is achieved using the PDB2PQR and PROPKA tools and noncovalent bond determination algorithms. A user-friendly interface allows visualizing pH-sensitive residues, affected salt bridges, hydrogen bonds and aromatic (pi\u2013pi and cation\u2013pi) interactions. patcHwork can be used to identify patches, a new concept we propose of pH-sensitive residues in close proximity on the protein, which may have a major impact on function. We demonstrate the attractiveness of patcHwork studying experimentally investigated pH-sensitive proteins\u00a0(https:\/\/patchwork.biologie.uni-freiburg.de\/).<\/jats:p>","DOI":"10.1093\/nar\/gkac252","type":"journal-article","created":{"date-parts":[[2022,4,14]],"date-time":"2022-04-14T07:18:52Z","timestamp":1649920732000},"page":"W560-W567","source":"Crossref","is-referenced-by-count":8,"title":["patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures"],"prefix":"10.1093","volume":"50","author":[{"given":"Mirko","family":"Schmitz","sequence":"first","affiliation":[{"name":"Signaling Research Centres BIOSS and CIBSS, University of Freiburg , Sch\u00e4nzlestr. 18, 79104 \u00a0 Freiburg , Germany"},{"name":"Institute of Biology II, University of Freiburg , Sch\u00e4nzlestr. 1, 79104 \u00a0 Freiburg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne","family":"Schultze","sequence":"additional","affiliation":[{"name":"Signaling Research Centres BIOSS and CIBSS, University of Freiburg , Sch\u00e4nzlestr. 18, 79104 \u00a0 Freiburg , Germany"},{"name":"Institute of Biology II, University of Freiburg , Sch\u00e4nzlestr. 1, 79104 \u00a0 Freiburg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raimonds","family":"Vanags","sequence":"additional","affiliation":[{"name":"Institute of Biology III, University of Freiburg , Sch\u00e4nzlestr. 1, 79104 \u00a0 Freiburg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karsten","family":"Voigt","sequence":"additional","affiliation":[{"name":"Institute of Biology III, University of Freiburg , Sch\u00e4nzlestr. 1, 79104 \u00a0 Freiburg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0247-9989","authenticated-orcid":false,"given":"Barbara","family":"Di\u00a0Ventura","sequence":"additional","affiliation":[{"name":"Signaling Research Centres BIOSS and CIBSS, University of Freiburg , Sch\u00e4nzlestr. 18, 79104 \u00a0 Freiburg , Germany"},{"name":"Institute of Biology II, University of Freiburg , Sch\u00e4nzlestr. 1, 79104 \u00a0 Freiburg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0840-1402","authenticated-orcid":false,"given":"Mehmet Ali","family":"\u00d6zt\u00fcrk","sequence":"additional","affiliation":[{"name":"Signaling Research Centres BIOSS and CIBSS, University of Freiburg , Sch\u00e4nzlestr. 18, 79104 \u00a0 Freiburg , Germany"},{"name":"Institute of Biology II, University of Freiburg , Sch\u00e4nzlestr. 1, 79104 \u00a0 Freiburg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,4,19]]},"reference":[{"key":"2022070423584467300_B1","doi-asserted-by":"crossref","first-page":"13285","DOI":"10.1074\/jbc.R800080200","article-title":"Protein ionizable groups: pK values and their contribution to protein stability and solubility","volume":"284","author":"Pace","year":"2009","journal-title":"J. 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