{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T03:47:49Z","timestamp":1790999269236,"version":"4.1.0"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Distinguishing between amyloid fibril-forming and amorphous \u03b2-aggregating aggregation-prone regions (APRs) in proteins and peptides is crucial for designing novel biomaterials and improved aggregation inhibitors for biotechnological and therapeutic purposes.<\/jats:p>\n               <jats:p>Results: Adjacent and alternate position residue pairs in hexapeptides show distinct preferences for occurrence in amyloid fibrils and amorphous \u03b2-aggregates. These observations were converted into energy potentials that were, in turn, machine learned. The resulting tool, called Generalized Aggregation Proneness (GAP), could successfully distinguish between amyloid fibril-forming and amorphous \u03b2-aggregating hexapeptides with almost 100 percent accuracies in validation tests performed using non-redundant datasets.<\/jats:p>\n               <jats:p>Conclusion: Accuracies of the predictions made by GAP are significantly improved compared with other methods capable of predicting either general \u03b2-aggregation or amyloid fibril-forming APRs. This work demonstrates that amino acid side chains play important roles in determining the morphological fate of \u03b2-mediated aggregates formed by short peptides.<\/jats:p>\n               <jats:p>Availability and implementation: \u00a0http:\/\/www.iitm.ac.in\/bioinfo\/GAP\/ .<\/jats:p>\n               <jats:p>Contact: \u00a0gromiha@iitm.ac.in<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu167","type":"journal-article","created":{"date-parts":[[2014,3,29]],"date-time":"2014-03-29T01:45:49Z","timestamp":1396057549000},"page":"1983-1990","source":"Crossref","is-referenced-by-count":63,"title":["GAP: towards almost 100 percent prediction for \u03b2-strand-mediated aggregating peptides with distinct morphologies"],"prefix":"10.1093","volume":"30","author":[{"given":"A. Mary","family":"Thangakani","sequence":"first","affiliation":[{"name":"1 Department of Crystallography and Biophysics, University of Madras, Chennai 600025, India, 2 Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Chesterfield, MO 63017, USA and 3 Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandeep","family":"Kumar","sequence":"additional","affiliation":[{"name":"1 Department of Crystallography and Biophysics, University of Madras, Chennai 600025, India, 2 Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Chesterfield, MO 63017, USA and 3 Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"R.","family":"Nagarajan","sequence":"additional","affiliation":[{"name":"1 Department of Crystallography and Biophysics, University of Madras, Chennai 600025, India, 2 Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Chesterfield, MO 63017, USA and 3 Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"D.","family":"Velmurugan","sequence":"additional","affiliation":[{"name":"1 Department of Crystallography and Biophysics, University of Madras, Chennai 600025, India, 2 Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Chesterfield, MO 63017, USA and 3 Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. Michael","family":"Gromiha","sequence":"additional","affiliation":[{"name":"1 Department of Crystallography and Biophysics, University of Madras, Chennai 600025, India, 2 Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Chesterfield, MO 63017, USA and 3 Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,3,28]]},"reference":[{"key":"2023012711241497100_btu167-B1","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1097\/WCO.0b013e328357bdf6","article-title":"Amyloid neuropathies","volume":"25","author":"Adams","year":"2012","journal-title":"Curr. Opin. 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