{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T19:46:55Z","timestamp":1784317615100,"version":"3.55.0"},"reference-count":44,"publisher":"Wiley","issue":"2","license":[{"start":{"date-parts":[[2022,10,3]],"date-time":"2022-10-03T00:00:00Z","timestamp":1664755200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/100019126","name":"Gujarat Council on Science and Technology","doi-asserted-by":"publisher","award":["GUJCOST\/Supercomputer\/2019\u201020\/1359"],"award-info":[{"award-number":["GUJCOST\/Supercomputer\/2019\u201020\/1359"]}],"id":[{"id":"10.13039\/100019126","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Proteins"],"published-print":{"date-parts":[[2023,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Understanding how MHC class II (MHC\u2010II) binding peptides with differing lengths exhibit specific interaction at the core and extended sites within the large MHC\u2010II pocket is a very important aspect of immunological research for designing peptides. Certain efforts were made to generate peptide conformations amenable for MHC\u2010II binding and calculate the binding energy of such complex formation but not directed toward developing a relationship between the peptide conformation in MHC\u2010II structures and the binding affinity (BA) (IC\n                    <jats:sub>50<\/jats:sub>\n                    ). We present here a machine\u2010learning approach to calculate the BA of the peptides within the MHC\u2010II pocket for HLA\u2010DRA1, HLA\u2010DRB1, HLA\u2010DP, and HLA\u2010DQ allotypes. Instead of generating ensembles of peptide conformations conventionally, the biased mode of conformations was created by considering the peptides in the crystal structures of pMHC\u2010II complexes as the templates, followed by site\u2010directed peptide docking. The structural interaction fingerprints generated from such docked pMHC\u2010II structures along with the Moran autocorrelation descriptors were trained using a random forest regressor specific to each MHC\u2010II peptide lengths (9\u201319). The entire workflow is automated using Linux shell and Perl scripts to promote the utilization of MHC2AffyPred program to any characterized MHC\u2010II allotypes and is made for free access at\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/github.com\/SiddhiJani\/pMHC2Pred\">https:\/\/github.com\/SiddhiJani\/MHC2AffyPred<\/jats:ext-link>\n                    . The MHC2AffyPred attained better performance (correlation coefficient [CC] of .612\u2013.898) than MHCII3D (.03\u2013.594) and NetMHCIIpan\u20103.2 (.289\u2013.692) programs in the HLA\u2010DRA1, HLA\u2010DRB1 types. Similarly, the MHC2AffyPred program achieved CC between .91 and .98 for HLA\u2010DP and HLA\u2010DQ peptides (13\u2010mer to 17\u2010mer). Further, a case study on MHC\u2010II binding 15\u2010mer peptides of severe acute respiratory syndrome coronavirus\u20102 showed very close competency in computing the IC\n                    <jats:sub>50<\/jats:sub>\n                    values compared to the sequence\u2010based NetMHCIIpan v3.2 and v4.0 programs with a correlation of .998 and .570, respectively.\n                  <\/jats:p>","DOI":"10.1002\/prot.26428","type":"journal-article","created":{"date-parts":[[2022,9,18]],"date-time":"2022-09-18T12:08:00Z","timestamp":1663502880000},"page":"277-289","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["<scp>MHC2AffyPred<\/scp>\n                    : A machine\u2010learning approach to estimate affinity of\n                    <scp>MHC<\/scp>\n                    class\n                    <scp>II<\/scp>\n                    peptides based on structural interaction fingerprints"],"prefix":"10.1002","volume":"91","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0693-419X","authenticated-orcid":false,"given":"Siddhi P.","family":"Jani","sequence":"first","affiliation":[{"name":"Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences Gujarat University  Ahmedabad Gujarat India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3461-2489","authenticated-orcid":false,"given":"Sivakumar Prasanth","family":"Kumar","sequence":"additional","affiliation":[{"name":"Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences Gujarat University  Ahmedabad Gujarat India"},{"name":"Department of Life Science, School of Sciences Gujarat University  Ahmedabad Gujarat India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9686-9429","authenticated-orcid":false,"given":"Naman","family":"Mangukia","sequence":"additional","affiliation":[{"name":"Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences Gujarat University  Ahmedabad Gujarat India"},{"name":"BioInnovations  Mumbai Maharashtra India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4919-1322","authenticated-orcid":false,"given":"Saumya K.","family":"Patel","sequence":"additional","affiliation":[{"name":"Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences Gujarat University  Ahmedabad Gujarat India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1912-3591","authenticated-orcid":false,"given":"Himanshu A.","family":"Pandya","sequence":"additional","affiliation":[{"name":"Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences Gujarat University  Ahmedabad Gujarat India"},{"name":"Department of Life Science, School of Sciences Gujarat University  Ahmedabad Gujarat India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7985-1187","authenticated-orcid":false,"given":"Rakesh M.","family":"Rawal","sequence":"additional","affiliation":[{"name":"Department of Life Science, School of Sciences Gujarat University  Ahmedabad Gujarat India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2022,10,3]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/s1074\u20107613(01)00202\u20103"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1086\/380997"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.4161\/onci.21205"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598\u2010020\u201067749\u20101"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.1186\/1472\u20106807\u201011\u201032"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/S41587\u2010019\u20100289\u20106"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.1007\/s002510050595"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00251\u2010004\u20100709\u20107"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1038\/9858"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365\u20102567.2012.03611.x"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471\u20102105\u20108\u2010238"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/17.12.1236"},{"key":"e_1_2_10_14_1","doi-asserted-by":"publisher","DOI":"10.2165\/00822942\u2010200605010\u201000008"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.1007\/S00251\u2010013\u20100720\u2010y"},{"key":"e_1_2_10_16_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471\u20102105\u201010\u2010296"},{"key":"e_1_2_10_17_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859\u2010019\u20102892\u20104"},{"key":"e_1_2_10_18_1","doi-asserted-by":"publisher","DOI":"10.1007\/978\u20101\u201060327\u2010118\u20109_14"},{"key":"e_1_2_10_19_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0030483"},{"key":"e_1_2_10_20_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00251\u2010015\u20100873\u2010y"},{"key":"e_1_2_10_21_1","doi-asserted-by":"publisher","DOI":"10.1093\/protein\/gzt018"},{"key":"e_1_2_10_22_1","doi-asserted-by":"publisher","DOI":"10.3390\/molecules24050881"},{"key":"e_1_2_10_23_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms22010012"},{"key":"e_1_2_10_24_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471\u20102105\u201011\u2010482"},{"key":"e_1_2_10_25_1","doi-asserted-by":"publisher","DOI":"10.1111\/imm.12889"},{"key":"e_1_2_10_26_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.10389"},{"key":"e_1_2_10_27_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv315"},{"key":"e_1_2_10_28_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu426"},{"key":"e_1_2_10_29_1","doi-asserted-by":"publisher","DOI":"10.1080\/00401706.1969.10490666"},{"key":"e_1_2_10_30_1","doi-asserted-by":"publisher","DOI":"10.1002\/bip.360270308"},{"key":"e_1_2_10_31_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13321\u2010016\u20100146\u20102"},{"key":"e_1_2_10_32_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.chemolab.2015.04.013"},{"key":"e_1_2_10_33_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki387"},{"key":"e_1_2_10_34_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2018.01.002"},{"key":"e_1_2_10_35_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.0c00305"},{"key":"e_1_2_10_36_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21256"},{"key":"e_1_2_10_37_1","doi-asserted-by":"publisher","DOI":"10.1186\/1758\u20102946\u20103\u201033"},{"key":"e_1_2_10_38_1","doi-asserted-by":"crossref","unstructured":"HolmesG 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