László Keresztes, Evelin Szögi, Bálint Varga, Viktor Farkas, András Perczel, Vince Grolmusz
Hexapeptides are increasingly applied as model systems for studying the amyloidogenic properties of oligo- and polypeptides. It is possible to construct 64 million different hexapeptides from the twenty proteinogenic amino acid residues. Today's experimental amyloid databases contain only a fraction of these annotated hexapeptides. For labeling all the possible hexapeptides as “amyloidogenic” or “non-amyloidogenic” there exist several computational predictors with good accuracy. It may be of interest to define and study a simple graph structure on the 64 million hexapeptides as nodes, when two hexapeptides are connected by an edge if they differ by only a single residue. For example, in this graph, HIKKLM is connected to AIKKLM, or HIKKNM, or HIKKLC, but it is not connected with an edge to VVKKLM or HIKNPM. In the present contribution, we consider our previously published artificial intelligence-based tool, the Budapest Amyloid Predictor (BAP for short), and demonstrate a spectacular property of this predictor in the graph defined above. We show that for any two hexapeptides predicted to be “amyloidogenic” by the BAP predictor, there exists an easily constructible path of length at most six that passes through neighboring hexapeptides all predicted to be “amyloidogenic” by BAP. For example, the predicted amyloidogenic ILVWIW and FWLCYL hexapeptides can be connected through the length-6 path ILVWIW-IWVWIW-IWVCIW-IWVCIL-FWVCIL-FWLCIL-FWLCYL in such a way that the neighbors differ in exactly one residue, and all hexapeptides on the path are predicted to be amyloidogenic by BAP. The symmetric statement also holds true for non-amyloidogenic predicted hexapeptides: For any such pair, there exists a path of length at most six, traversing only predicted non-amyloidogenic hexapeptides. It is noted that the mentioned property of the Budapest Amyloid Predictor https://pitgroup.org/bap is not proprietary; it is also true for any linear Support Vector Machine (SVM)-based predictors; therefore, for any future improvements of BAP using the linear SVM prediction technique.
{"title":"Navigating Homogeneous Graph Paths Through Amyloidogenic and Non-Amyloidogenic Hexapeptides","authors":"László Keresztes, Evelin Szögi, Bálint Varga, Viktor Farkas, András Perczel, Vince Grolmusz","doi":"10.1002/jcc.70238","DOIUrl":"10.1002/jcc.70238","url":null,"abstract":"<p>Hexapeptides are increasingly applied as model systems for studying the amyloidogenic properties of oligo- and polypeptides. It is possible to construct 64 million different hexapeptides from the twenty proteinogenic amino acid residues. Today's experimental amyloid databases contain only a fraction of these annotated hexapeptides. For labeling all the possible hexapeptides as “amyloidogenic” or “non-amyloidogenic” there exist several computational predictors with good accuracy. It may be of interest to define and study a simple graph structure on the 64 million hexapeptides as nodes, when two hexapeptides are connected by an edge if they differ by only a single residue. For example, in this graph, HIKKLM is connected to AIKKLM, or HIKKNM, or HIKKLC, but it is not connected with an edge to VVKKLM or HIKNPM. In the present contribution, we consider our previously published artificial intelligence-based tool, the Budapest Amyloid Predictor (BAP for short), and demonstrate a spectacular property of this predictor in the graph defined above. We show that for any two hexapeptides predicted to be “amyloidogenic” by the BAP predictor, there exists an easily constructible path of length at most six that passes through neighboring hexapeptides all predicted to be “amyloidogenic” by BAP. For example, the predicted amyloidogenic ILVWIW and FWLCYL hexapeptides can be connected through the length-6 path ILVWIW-IWVWIW-IWVCIW-IWVCIL-FWVCIL-FWLCIL-FWLCYL in such a way that the neighbors differ in exactly one residue, and all hexapeptides on the path are predicted to be amyloidogenic by BAP. The symmetric statement also holds true for non-amyloidogenic predicted hexapeptides: For any such pair, there exists a path of length at most six, traversing only predicted non-amyloidogenic hexapeptides. It is noted that the mentioned property of the Budapest Amyloid Predictor https://pitgroup.org/bap is not proprietary; it is also true for any linear Support Vector Machine (SVM)-based predictors; therefore, for any future improvements of BAP using the linear SVM prediction technique.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 26","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70238","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145209454","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Biswas, B. C., Shimul, A. I., Ghosh, A., Awaad, N. S., and Ibrahium, H. A., “Exploring Lead-Free Ca3BiCl3-Based Perovskite Solar Cells: A Computational Comparison of Charge Transport Layers With DFT and SCAPS-1D,” Journal of Computational Chemistry 46 (2025): e70231, https://doi.org/10.1002/jcc.70231.
The acknowledgment section has been changed as below:
The authors extend their appreciation to the Deanship of Research and Graduate Studies at King Khalid University for funding this work through Large Research Project under grant number RGP2/338/46.
We apologize for this error.
Biswas, b.c, Shimul, a.i, Ghosh, A., Awaad, N. S.和Ibrahium, H. A.,“探索无铅ca3bicl3 -钙钛矿太阳能电池:基于DFT和SCAPS-1D的电荷传输层的计算比较”,计算化学杂志46 (2025):e70231, https://doi.org/10.1002/jcc.70231.The致谢部分更改如下:作者感谢哈立德国王大学研究与研究生院院长通过大型研究项目资助本工作,资助号为RGP2/338/46。我们为这个错误道歉。
{"title":"Correction to “Exploring Lead-Free Ca3BiCl3-Based Perovskite Solar Cells: A Computational Comparison of Charge Transport Layers With DFT and SCAPS-1D”","authors":"","doi":"10.1002/jcc.70247","DOIUrl":"10.1002/jcc.70247","url":null,"abstract":"<p>Biswas, B. C., Shimul, A. I., Ghosh, A., Awaad, N. S., and Ibrahium, H. A., “Exploring Lead-Free Ca<sub>3</sub>BiCl<sub>3</sub>-Based Perovskite Solar Cells: A Computational Comparison of Charge Transport Layers With DFT and SCAPS-1D,” <i>Journal of Computational Chemistry</i> 46 (2025): e70231, https://doi.org/10.1002/jcc.70231.</p><p>The acknowledgment section has been changed as below:</p><p>The authors extend their appreciation to the Deanship of Research and Graduate Studies at King Khalid University for funding this work through Large Research Project under grant number RGP2/338/46.</p><p>We apologize for this error.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 25","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70247","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145189448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}