{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,27]],"date-time":"2026-04-27T17:47:06Z","timestamp":1777312026143,"version":"3.51.4"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,5,9]],"date-time":"2023-05-09T00:00:00Z","timestamp":1683590400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009122","name":"Ministry of Education","doi-asserted-by":"publisher","award":["LM2023055"],"award-info":[{"award-number":["LM2023055"]}],"id":[{"id":"10.13039\/100009122","id-type":"DOI","asserted-by":"publisher"}]},{"name":"IOCB Tech Foundation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The AlphaFold2 prediction algorithm opened up the possibility of exploring proteins\u2019 structural space at an unprecedented scale. Currently, &amp;gt;200 million protein structures predicted by this approach are deposited in AlphaFoldDB, covering entire proteomes of multiple organisms, including humans. Predicted structures are, however, stored without detailed functional annotations describing their chemical behaviour. Partial atomic charges, which map electron distribution over a molecule and provide a clue to its chemical reactivity, are an important example of such data. We introduce the web application \u03b1Charges: a tool for the quick calculation of partial atomic charges for protein structures from AlphaFoldDB. The charges are calculated by the recent empirical method SQE+qp, parameterised for this class of molecules using robust quantum mechanics charges (B3LYP\/6-31G*\/NPA) on PROPKA3 protonated structures. The computed partial atomic charges can be downloaded in common data formats or visualised via the powerful Mol* viewer.\u00a0The \u03b1Charges application is freely available at https:\/\/alphacharges.ncbr.muni.cz with no login requirement.<\/jats:p>","DOI":"10.1093\/nar\/gkad349","type":"journal-article","created":{"date-parts":[[2023,5,10]],"date-time":"2023-05-10T19:37:30Z","timestamp":1683747450000},"page":"W11-W16","source":"Crossref","is-referenced-by-count":4,"title":["\u03b1Charges: partial atomic charges for AlphaFold structures in high quality"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9047-0334","authenticated-orcid":false,"given":"Ond\u0159ej","family":"Schindler","sequence":"first","affiliation":[{"name":"CEITEC \u2013 Central European Institute of Technology, Masaryk University , 625 00 Brno, Czech Republic"},{"name":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University , 625 00 Brno, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9472-2589","authenticated-orcid":false,"given":"Karel","family":"Berka","sequence":"additional","affiliation":[{"name":"Department of Physical Chemistry, Faculty of Science, Palack\u00fd University Olomouc , 779 00 Olomouc, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3619-6434","authenticated-orcid":false,"given":"Alessio","family":"Cantara","sequence":"additional","affiliation":[{"name":"CEITEC \u2013 Central European Institute of Technology, Masaryk University , 625 00 Brno, Czech Republic"},{"name":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University , 625 00 Brno, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3395-3196","authenticated-orcid":false,"given":"Ale\u0161","family":"K\u0159enek","sequence":"additional","affiliation":[{"name":"Institute of Computer Science, Masaryk University , 602 00 Brno, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7266-1789","authenticated-orcid":false,"given":"Dominik","family":"Tich\u00fd","sequence":"additional","affiliation":[{"name":"Faculty of Informatics, Masaryk University , 602 00 Brno, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0296-2452","authenticated-orcid":false,"given":"Tom\u00e1\u0161","family":"Ra\u010dek","sequence":"additional","affiliation":[{"name":"CEITEC \u2013 Central European Institute of Technology, Masaryk University , 625 00 Brno, Czech Republic"},{"name":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University , 625 00 Brno, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3840-8760","authenticated-orcid":false,"given":"Radka","family":"Svobodov\u00e1","sequence":"additional","affiliation":[{"name":"CEITEC \u2013 Central European Institute of Technology, Masaryk University , 625 00 Brno, Czech Republic"},{"name":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University , 625 00 Brno, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,5,9]]},"reference":[{"key":"2023070505002335000_B1","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"2023070505002335000_B2","doi-asserted-by":"crossref","first-page":"e4439","DOI":"10.1002\/pro.4439","article-title":"PDBe and PDBe-KB: providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education","volume":"31","author":"Varadi","year":"2022","journal-title":"Protein Sci."},{"key":"2023070505002335000_B3","doi-asserted-by":"crossref","first-page":"D439","DOI":"10.1093\/nar\/gkab1061","article-title":"AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models","volume":"50","author":"Varadi","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2023070505002335000_B4","doi-asserted-by":"crossref","first-page":"W591","DOI":"10.1093\/nar\/gkaa367","article-title":"Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges","volume":"48","author":"Ra\u010dek","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2023070505002335000_B5","doi-asserted-by":"crossref","first-page":"880","DOI":"10.1021\/jp003449n","article-title":"Electrostatic complementarity at ligand binding sites: application to chorismate mutase","volume":"105","author":"Kangas","year":"2001","journal-title":"J. Phys. Chem. B"},{"key":"2023070505002335000_B6","doi-asserted-by":"crossref","first-page":"3022","DOI":"10.1002\/anie.200502530","article-title":"Why are proteins charged? Networks of charge\u2013charge interactions in proteins measured by charge ladders and capillary electrophoresis","volume":"45","author":"Gitlin","year":"2006","journal-title":"Angew. Chem."},{"key":"2023070505002335000_B7","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1002\/prot.21183","article-title":"Critical assessment of the automated AutoDock as a new docking tool for virtual screening","volume":"65","author":"Park","year":"2006","journal-title":"Proteins"},{"key":"2023070505002335000_B8","doi-asserted-by":"crossref","first-page":"3358","DOI":"10.1021\/j100161a070","article-title":"Charge equilibration for molecular dynamics simulations","volume":"95","author":"Rapp\u00e9","year":"1991","journal-title":"J. Phys. Chem."},{"key":"2023070505002335000_B9","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1021\/acs.chemmater.5b03836","article-title":"A comprehensive set of high-quality point charges for simulations of metal\u2013organic frameworks","volume":"28","author":"Nazarian","year":"2016","journal-title":"Chem. Mater."},{"key":"2023070505002335000_B10","doi-asserted-by":"crossref","first-page":"046702","DOI":"10.1103\/PhysRevE.69.046702","article-title":"Computing induced charges in inhomogeneous dielectric media: application in a Monte Carlo simulation of complex ionic systems","volume":"69","author":"Boda","year":"2004","journal-title":"Phys. Rev. E"},{"key":"2023070505002335000_B11","volume-title":"Principles of Quantum Mechanics","author":"Shankar","year":"2012"},{"key":"2023070505002335000_B12","doi-asserted-by":"crossref","first-page":"4066","DOI":"10.1063\/1.445134","article-title":"Natural bond orbital analysis of near-Hartree\u2013Fock water dimer","volume":"78","author":"Reed","year":"1983","journal-title":"J. Chem. Phys."},{"key":"2023070505002335000_B13","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1063\/1.449486","article-title":"Natural population analysis","volume":"83","author":"Reed","year":"1985","journal-title":"J. Chem. Phys."},{"key":"2023070505002335000_B14","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1186\/s13321-021-00528-w","article-title":"Optimized SQE atomic charges for peptides accessible via a web application","volume":"13","author":"Schindler","year":"2021","journal-title":"J. Cheminform."},{"key":"2023070505002335000_B15","doi-asserted-by":"crossref","first-page":"2284","DOI":"10.1021\/ct200133y","article-title":"Improved treatment of ligands and coupling effects in empirical calculation and rationalization of pKa values","volume":"7","author":"S\u00f8ndergaard","year":"2011","journal-title":"J. Chem. Theory Comput."},{"key":"2023070505002335000_B16","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1021\/ct100578z","article-title":"PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions","volume":"7","author":"Olsson","year":"2011","journal-title":"J. Chem. Theory Comput."},{"key":"2023070505002335000_B17","doi-asserted-by":"crossref","first-page":"W431","DOI":"10.1093\/nar\/gkab314","article-title":"Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures","volume":"49","author":"Sehnal","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2023070505002335000_B18","doi-asserted-by":"crossref","first-page":"D437","DOI":"10.1093\/nar\/gkaa1038","article-title":"RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences","volume":"49","author":"Burley","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2023070505002335000_B19","doi-asserted-by":"crossref","first-page":"4315","DOI":"10.1021\/ja00275a013","article-title":"Electronegativity equalization method for the calculation of atomic charges in molecules","volume":"108","author":"Mortier","year":"1986","journal-title":"J. Am. Chem. Soc."},{"key":"2023070505002335000_B20","doi-asserted-by":"crossref","first-page":"094108","DOI":"10.1063\/1.2346671","article-title":"A generalization of the charge equilibration method for nonmetallic materials","volume":"125","author":"Nistor","year":"2006","journal-title":"J. Chem. Phys."},{"key":"2023070505002335000_B21","doi-asserted-by":"crossref","first-page":"W665","DOI":"10.1093\/nar\/gkh381","article-title":"PDB2PQR: an automated pipeline for the setup of Poisson\u2013Boltzmann electrostatics calculations","volume":"32","author":"Dolinsky","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023070505002335000_B22","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1186\/s13321-015-0099-x","article-title":"AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules","volume":"7","author":"Ionescu","year":"2015","journal-title":"J. Cheminform."},{"key":"2023070505002335000_B23","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1016\/j.taap.2004.10.012","article-title":"Multidrug resistance proteins: role of P-glycoprotein, MRP1, MRP2, and BCRP (ABCG2) in tissue defense","volume":"204","author":"Leslie","year":"2005","journal-title":"Toxicol. Appl. Pharmacol."},{"key":"2023070505002335000_B24","doi-asserted-by":"crossref","first-page":"13386","DOI":"10.1073\/pnas.1309275110","article-title":"Structures of P-glycoprotein reveal its conformational flexibility and an epitope on the nucleotide-binding domain","volume":"110","author":"Ward","year":"2013","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2023070505002335000_B25","article-title":"Physiology, pepsin","volume-title":"StatPearls","author":"Heda","year":"2022"},{"key":"2023070505002335000_B26","doi-asserted-by":"crossref","first-page":"31","DOI":"10.21037\/aoe-20-95","article-title":"Pepsin properties, structure, and its accurate measurement: a narrative review","volume":"5","author":"Stanforth","year":"2022","journal-title":"Ann. Esophagus"},{"key":"2023070505002335000_B27","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1093\/protein\/14.9.669","article-title":"N-terminal portion acts as an initiator of the inactivation of pepsin at neutral pH","volume":"14","author":"Tanaka","year":"2001","journal-title":"Protein Eng. Des. Sel."},{"key":"2023070505002335000_B28","doi-asserted-by":"crossref","first-page":"109871","DOI":"10.1016\/j.enzmictec.2021.109871","article-title":"Improving the alkaline stability of pepsin through rational protein design using renin, an alkaline-stable aspartic protease, as a structural and functional reference","volume":"150","author":"Grahame","year":"2021","journal-title":"Enzyme Microb. Technol."},{"key":"2023070505002335000_B29","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1038\/s41586-022-04883-y","article-title":"Structures and mechanism of the plant PIN-FORMED auxin transporter","volume":"609","author":"Ung","year":"2022","journal-title":"Nature"},{"key":"2023070505002335000_B30","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1038\/s41586-022-05143-9","article-title":"Structural insights into auxin recognition and efflux by Arabidopsis PIN1","volume":"609","author":"Yang","year":"2022","journal-title":"Nature"},{"key":"2023070505002335000_B31","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1038\/s41586-022-05142-w","article-title":"Structures and mechanisms of the Arabidopsis auxin transporter PIN3","volume":"609","author":"Su","year":"2022","journal-title":"Nature"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/W1\/W11\/50736711\/gkad349.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/W1\/W11\/50736711\/gkad349.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,5]],"date-time":"2023-07-05T10:32:03Z","timestamp":1688553123000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/51\/W1\/W11\/7157525"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,5,9]]},"references-count":31,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2023,5,9]]},"published-print":{"date-parts":[[2023,7,5]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkad349","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,7,5]]},"published":{"date-parts":[[2023,5,9]]}}}