{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T22:16:57Z","timestamp":1793225817215,"version":"4.5.0"},"reference-count":53,"publisher":"Springer Science and Business Media LLC","license":[{"start":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T00:00:00Z","timestamp":1790294400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T00:00:00Z","timestamp":1790294400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Mol Divers"],"DOI":"10.1007\/s11030-026-11710-3","type":"journal-article","created":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T13:50:21Z","timestamp":1790344221000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["In silico directed evolution of humanized peptide transporters via computational epistatic rescue"],"prefix":"10.1007","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-7864-0732","authenticated-orcid":false,"given":"Alper","family":"Karag\u00f6l","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-1011-7661","authenticated-orcid":false,"given":"Taner","family":"Karag\u00f6l","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,25]]},"reference":[{"issue":"5","key":"11710_CR1","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1007\/s00232-025-00348-1","volume":"258","author":"T Roy","year":"2025","unstructured":"Roy T, Nath M, Halder N, Saxena R, Velpandian T (2025) Functional and physiological implications of oligopeptide transporters: potential targets for pharmacological interventions. J Membr Biol 258(5):375\u2013390. https:\/\/doi.org\/10.1007\/s00232-025-00348-1","journal-title":"J Membr Biol"},{"key":"11710_CR2","volume-title":"Drug Transporters","author":"JM Jordan","year":"2025","unstructured":"Jordan JM, Ersoy BA (2025) Drug Transporters. The Pathophysiologic Basis of Drug Therapy, Principles of Pharmacology"},{"issue":"2\u20133","key":"11710_CR3","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1016\/j.mam.2012.11.003","volume":"34","author":"DE Smith","year":"2013","unstructured":"Smith DE, Cl\u00e9men\u00e7on B, Hediger MA (2013) Proton-coupled oligopeptide transporter family SLC15: physiological, pharmacological and pathological implications. Mol Aspects Med 34(2\u20133):323\u2013336. https:\/\/doi.org\/10.1016\/j.mam.2012.11.003","journal-title":"Mol Aspects Med"},{"issue":"8010","key":"11710_CR4","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1038\/s41586-024-07290-7","volume":"629","author":"J Ye","year":"2024","unstructured":"Ye J, Chen H, Wang K, Wang Y, Ammerman A, Awasthi S, Xu J, Liu B, Li W (2024) Structural insights into vesicular monoamine storage and drug interactions. Nature 629(8010):235\u2013243. https:\/\/doi.org\/10.1038\/s41586-024-07290-7","journal-title":"Nature"},{"issue":"5","key":"11710_CR5","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1007\/s13238-016-0263-8","volume":"7","author":"X Lv","year":"2016","unstructured":"Lv X, Liu J, Shi Q, Tan Q, Wu D, Skinner JJ, Walker AL, Zhao L, Gu X, Chen N, Xue L, Si P, Zhang L, Wang Z, Katritch V, Liu ZJ, Stevens RC (2016) In vitro expression and analysis of the 826 human G protein-coupled receptors. Protein Cell 7(5):325\u2013337. https:\/\/doi.org\/10.1007\/s13238-016-0263-8","journal-title":"Protein Cell"},{"issue":"5","key":"11710_CR6","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1016\/j.sbi.2008.07.001","volume":"18","author":"EP Carpenter","year":"2008","unstructured":"Carpenter EP, Beis K, Cameron AD, Iwata S (2008) Overcoming the challenges of membrane protein crystallography. Curr Opin Struct Biol 18(5):581\u2013586. https:\/\/doi.org\/10.1016\/j.sbi.2008.07.001","journal-title":"Curr Opin Struct Biol"},{"issue":"37","key":"11710_CR7","doi-asserted-by":"publisher","first-page":"E8652","DOI":"10.1073\/pnas.1811031115","volume":"115","author":"S Zhang","year":"2018","unstructured":"Zhang S, Tao F, Qing R, Tang H, Skuhersky M, Corin K, Maertens B (2018) QTY code enables design of detergent-free chemokine receptors that retain ligand-binding activities. Proc Natl Acad Sci 115(37):E8652\u2013E8659. https:\/\/doi.org\/10.1073\/pnas.1811031115","journal-title":"Proc Natl Acad Sci"},{"issue":"3","key":"11710_CR8","doi-asserted-by":"publisher","first-page":"e0300340","DOI":"10.1371\/journal.pone.0300340","volume":"19","author":"T Karag\u00f6l","year":"2024","unstructured":"Karag\u00f6l T, Karag\u00f6l A, Zhang S (2024) Structural bioinformatics studies of serotonin, dopamine and norepinephrine transporters and their AlphaFold2 predicted water-soluble QTY variants and uncovering the natural mutations of L-> Q, I-> T, F-> Y and Q-> L, T-> I and Y-> F. PLoS ONE 19(3):e0300340. https:\/\/doi.org\/10.1371\/journal.pone.0300340","journal-title":"PLoS ONE"},{"key":"11710_CR9","doi-asserted-by":"publisher","first-page":"e1","DOI":"10.1017\/qrd.2024.2.pr1","volume":"5","author":"E Pan","year":"2024","unstructured":"Pan E, Tao F, Smorodina E, Zhang S (2024) Structural bioinformatics studies of six human ABC transporters and their AlphaFold2-predicted water-soluble QTY variants. QRB discovery 5:e1. https:\/\/doi.org\/10.1017\/qrd.2024.2.pr1","journal-title":"QRB discovery"},{"key":"11710_CR10","doi-asserted-by":"publisher","first-page":"917725","DOI":"10.3389\/fmolb.2022.917725","volume":"9","author":"M Killer","year":"2022","unstructured":"Killer M, Finocchio G, Mertens HD, Svergun DI, Pardon E, Steyaert J, L\u00f6w C (2022) Cryo-EM structure of an atypical proton-coupled peptide transporter: di-and tripeptide permease C. Front Mol Biosci 9:917725. https:\/\/doi.org\/10.3389\/fmolb.2022.917725","journal-title":"Front Mol Biosci"},{"issue":"1","key":"11710_CR11","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1038\/s42004-022-00636-0","volume":"5","author":"M Stauffer","year":"2022","unstructured":"Stauffer M, Jeckelmann JM, Ilg\u00fc H, Ucurum Z, Boggavarapu R, Fotiadis D (2022) Peptide transporter structure reveals binding and action mechanism of a potent PEPT1 and PEPT2 inhibitor. Commun Chem 5(1):23. https:\/\/doi.org\/10.1038\/s42004-022-00636-0","journal-title":"Commun Chem"},{"issue":"5","key":"11710_CR12","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1128\/aac.02307-18","volume":"63","author":"JB Bulitta","year":"2019","unstructured":"Bulitta JB, Hope WW, Eakin AE, Guina T, Tam VH, Louie A, Hoover JL (2019) Generating robust and informative nonclinical in vitro and in vivo bacterial infection model efficacy data to support translation to humans. Antimicrob Agents Chemother 63(5):10\u20131128. https:\/\/doi.org\/10.1128\/aac.02307-18","journal-title":"Antimicrob Agents Chemother"},{"key":"11710_CR13","doi-asserted-by":"publisher","first-page":"88","DOI":"10.3389\/fmolb.2020.00088","volume":"7","author":"M Ayyildiz","year":"2020","unstructured":"Ayyildiz M, Celiker S, Ozhelvaci F, Akten ED (2020) Identification of alternative allosteric sites in glycolytic enzymes for potential use as species-specific drug targets. Front Mol Biosci 7:88. https:\/\/doi.org\/10.3389\/fmolb.2020.00088","journal-title":"Front Mol Biosci"},{"issue":"3","key":"11710_CR14","doi-asserted-by":"publisher","first-page":"354","DOI":"10.1016\/j.tibtech.2021.08.002","volume":"40","author":"MK Heavey","year":"2022","unstructured":"Heavey MK, Durmusoglu D, Crook N, Anselmo AC (2022) Discovery and delivery strategies for engineered live biotherapeutic products. Trends Biotechnol 40(3):354\u2013369. https:\/\/doi.org\/10.1016\/j.tibtech.2021.08.002","journal-title":"Trends Biotechnol"},{"issue":"9","key":"11710_CR15","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1007\/s00203-025-04417-w","volume":"207","author":"S Sadhu","year":"2025","unstructured":"Sadhu S, Paul T, Yadav N (2025) Therapeutic engineering of the gut microbiome using synthetic biology and metabolic tools: a comprehensive review with E. coli Nissle 1917 as a model case study. Arch Microbiol 207(9):213. https:\/\/doi.org\/10.1007\/s00203-025-04417-w","journal-title":"Arch Microbiol"},{"issue":"20","key":"11710_CR16","doi-asserted-by":"publisher","first-page":"8693","DOI":"10.1007\/s00253-016-7829-5","volume":"100","author":"B Ou","year":"2016","unstructured":"Ou B, Yang Y, Tham WL, Chen L, Guo J, Zhu G (2016) Genetic engineering of probiotic Escherichia coli Nissle 1917 for clinical application. Appl Microbiol Biotechnol 100(20):8693\u20138699. https:\/\/doi.org\/10.1007\/s00253-016-7829-5","journal-title":"Appl Microbiol Biotechnol"},{"issue":"9","key":"11710_CR17","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1016\/j.tips.2022.02.002","volume":"43","author":"JP Lynch","year":"2022","unstructured":"Lynch JP, Goers L, Lesser CF (2022) Emerging strategies for engineering Escherichia coli Nissle 1917-based therapeutics. Trends Pharmacol Sci 43(9):772\u2013786. https:\/\/doi.org\/10.1016\/j.tips.2022.02.002","journal-title":"Trends Pharmacol Sci"},{"issue":"12","key":"11710_CR18","doi-asserted-by":"publisher","first-page":"e00269","DOI":"10.1128\/jb.00269-24","volume":"206","author":"C Clare","year":"2024","unstructured":"Clare C, Rutter JW, Fedorec AJ, Frank S, Barnes CP (2024) Bacterial microcompartment utilization in the human commensal Escherichia coli Nissle 1917. J Bacteriol 206(12):e00269\u2013e00224. https:\/\/doi.org\/10.1128\/jb.00269-24","journal-title":"J Bacteriol"},{"issue":"3","key":"11710_CR19","doi-asserted-by":"publisher","first-page":"456a","DOI":"10.1016\/j.bpj.2021.11.488","volume":"121","author":"NJ Ose","year":"2022","unstructured":"Ose NJ, Campitelli P, Patel RP, Ozkan SB, Kumar S (2022) Protein dynamics provide mechanistic insights about the epistatic relationships among highly observed potentially adaptive missense variants. Biophys J 121(3):456a. https:\/\/doi.org\/10.1016\/j.bpj.2021.11.488","journal-title":"Biophys J"},{"issue":"9","key":"11710_CR20","doi-asserted-by":"publisher","first-page":"751","DOI":"10.1016\/j.tibs.2023.05.009","volume":"48","author":"K Buda","year":"2023","unstructured":"Buda K, Miton CM, Fan XC, Tokuriki N (2023) Molecular determinants of protein evolvability. Trends Biochem Sci 48(9):751\u2013760. https:\/\/doi.org\/10.1016\/j.tibs.2023.05.009","journal-title":"Trends Biochem Sci"},{"key":"11710_CR21","doi-asserted-by":"publisher","unstructured":"Tharp CR, Catalano C, Khalifeh A, Ghaffari-Kashani S, Huang R, Kang G, Phillips AM (2026) Biophysical trade-offs in antibody evolution are resolved by conformation-mediated epistasis. https:\/\/doi.org\/10.64898\/2026.03.12.711465. bioRxiv, 2026-03","DOI":"10.64898\/2026.03.12.711465"},{"issue":"5","key":"11710_CR22","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1007\/s00239-025-10262-8","volume":"93","author":"T Karag\u00f6l","year":"2025","unstructured":"Karag\u00f6l T, Karag\u00f6l A, Zhang S (2025) Co-evolution of alpha-helical transmembrane protein residues: large-scale variant profiling and complete mutational landscape of 2277 known PDB entries representing 504 unique human protein sequences. J Mol Evol 93(5):581\u2013599. https:\/\/doi.org\/10.1007\/s00239-025-10262-8","journal-title":"J Mol Evol"},{"issue":"1","key":"11710_CR23","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1186\/s13068-024-02457-w","volume":"17","author":"S Chen","year":"2024","unstructured":"Chen S, Yang Z, Zhong Z, Yu S, Zhou J, Li J, Zhang G (2024) Ultrahigh-throughput screening-assisted in vivo directed evolution for enzyme engineering. Biotechnol Biofuels Bioprod 17(1):9. https:\/\/doi.org\/10.1186\/s13068-024-02457-w","journal-title":"Biotechnol Biofuels Bioprod"},{"issue":"5","key":"11710_CR24","doi-asserted-by":"publisher","first-page":"378","DOI":"10.1016\/j.trechm.2022.02.004","volume":"4","author":"RJ McLure","year":"2022","unstructured":"McLure RJ, Radford SE, Brockwell DJ (2022) High-throughput directed evolution: a golden era for protein science. Trends Chem 4(5):378\u2013391. https:\/\/doi.org\/10.1016\/j.trechm.2022.02.004","journal-title":"Trends Chem"},{"issue":"20","key":"11710_CR25","doi-asserted-by":"publisher","first-page":"12384","DOI":"10.1021\/acs.chemrev.1c00260","volume":"121","author":"Y Wang","year":"2021","unstructured":"Wang Y, Xue P, Cao M, Yu T, Lane ST, Zhao H (2021) Directed evolution: methodologies and applications. Chem Rev 121(20):12384\u201312444. https:\/\/doi.org\/10.1021\/acs.chemrev.1c00260","journal-title":"Chem Rev"},{"issue":"6637","key":"11710_CR26","doi-asserted-by":"publisher","first-page":"1123","DOI":"10.1126\/science.ade2574","volume":"379","author":"Z Lin","year":"2023","unstructured":"Lin Z, Akin H, Rao R, Hie B, Zhu Z, Lu W, Rives A (2023) Evolutionary-scale prediction of atomic-level protein structure with a language model. Science 379(6637):1123\u20131130. https:\/\/doi.org\/10.1126\/science.ade2574","journal-title":"Science"},{"key":"11710_CR27","doi-asserted-by":"publisher","first-page":"e2","DOI":"10.1017\/qrd.2024.18","volume":"6","author":"F Johnsson","year":"2025","unstructured":"Johnsson F, Karag\u00f6l T, Karag\u00f6l A, Zhang S (2025) Structural bioinformatic study of six human olfactory receptors and their AlphaFold3 predicted water-soluble QTY variants and OR1A2 with an odorant octanoate and TAAR9 with spermidine. QRB discovery 6:e2. https:\/\/doi.org\/10.1017\/qrd.2024.18","journal-title":"QRB discovery"},{"issue":"10","key":"11710_CR28","doi-asserted-by":"publisher","first-page":"1965","DOI":"10.1007\/s11095-024-03769-0","volume":"41","author":"A Karag\u00f6l","year":"2024","unstructured":"Karag\u00f6l A, Karag\u00f6l T, Zhang S (2024) Molecular dynamic simulations reveal that water-soluble QTY-Variants of glutamate transporters EAA1, EAA2 and EAA3 retain the conformational characteristics of native transporters. Pharm Res 41(10):1965\u20131977. https:\/\/doi.org\/10.1007\/s11095-024-03769-0","journal-title":"Pharm Res"},{"issue":"11","key":"11710_CR29","doi-asserted-by":"publisher","first-page":"2173","DOI":"10.1007\/s11095-024-03786-z","volume":"41","author":"A Karag\u00f6l","year":"2024","unstructured":"Karag\u00f6l A, Karag\u00f6l T, Li M, Zhang S (2024) Inhibitory Potential of the Truncated Isoforms on Glutamate Transporter Oligomerization Identified by Computational Analysis of Gene-Centric Isoform Maps. Pharm Res 41(11):2173\u20132187. https:\/\/doi.org\/10.1007\/s11095-024-03786-z","journal-title":"Pharm Res"},{"key":"11710_CR30","doi-asserted-by":"publisher","unstructured":"Karag\u00f6l A, Karag\u00f6l T, Zhang S (2026) Integrative Structural Bioinformatics and Molecular Dynamics Analyses of Synaptic Vesicle Proteins and Their Water-Soluble QTY-Variants Reveal Membrane Constraints and Evolutionary Coupling of T \u21d4 V. J. Mol. Evol.https:\/\/doi.org\/10.1007\/s00239-026-10315-6","DOI":"10.1007\/s00239-026-10315-6"},{"issue":"15","key":"11710_CR31","doi-asserted-by":"publisher","first-page":"984","DOI":"10.1080\/08927022.2025.2562932","volume":"51","author":"A Sajeev-Sheeja","year":"2025","unstructured":"Sajeev-Sheeja A, Karag\u00f6l A, Karag\u00f6l T, Zhang S (2025) Molecular dynamics simulations and structural bioinformatics of bacterial integral alpha-helical membrane enzymes and their AlphaFold2-predicted water-soluble QTY analogues. Mol Simul 51(15):984\u2013998. https:\/\/doi.org\/10.1080\/08927022.2025.2562932","journal-title":"Mol Simul"},{"key":"11710_CR32","doi-asserted-by":"publisher","unstructured":"Karag\u00f6l T, Karag\u00f6l A (2025) pH-dependent membrane binding specificity of synaptogyrins 1\u20133 provides mechanistic insights into synaptic vesicle regulation and neurological disease. https:\/\/doi.org\/10.1101\/2025.03.03.641025. bioRxiv 2025.03.03.641025","DOI":"10.1101\/2025.03.03.641025"},{"issue":"10","key":"11710_CR33","doi-asserted-by":"publisher","first-page":"790","DOI":"10.1016\/j.tips.2019.08.006","volume":"40","author":"RAA Garibsingh","year":"2019","unstructured":"Garibsingh RAA, Schlessinger A (2019) Advances and challenges in rational drug design for SLCs. Trends Pharmacol Sci 40(10):790\u2013800. https:\/\/doi.org\/10.1016\/j.tips.2019.08.006","journal-title":"Trends Pharmacol Sci"},{"issue":"2","key":"11710_CR34","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1038\/s41587-023-01987-2","volume":"42","author":"H Li","year":"2024","unstructured":"Li H, Sun X, Cui W, Xu M, Dong J, Ekundayo BE, Vogel H (2024) Computational drug development for membrane protein targets. Nat Biotechnol 42(2):229\u2013242. https:\/\/doi.org\/10.1038\/s41587-023-01987-2","journal-title":"Nat Biotechnol"},{"issue":"1","key":"11710_CR35","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1007\/s40495-025-00424-z","volume":"11","author":"N Das","year":"2025","unstructured":"Das N, Singh S, Swaminathan P (2025) Rational drug designing for antimicrobial resistance: new strategies and targets. Curr Pharmacol Rep 11(1):44. https:\/\/doi.org\/10.1007\/s40495-025-00424-z","journal-title":"Curr Pharmacol Rep"},{"issue":"11","key":"11710_CR36","doi-asserted-by":"publisher","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","volume":"25","author":"PJ Cock","year":"2009","unstructured":"Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, De Hoon MJ (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25(11):1422. https:\/\/doi.org\/10.1093\/bioinformatics\/btp163","journal-title":"Bioinformatics"},{"issue":"1","key":"11710_CR37","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1007\/s11095-006-9119-x","volume":"24","author":"AA Kulkarni","year":"2007","unstructured":"Kulkarni AA, Davies DL, Links JS, Patel LN, Lee VH, Haworth IS (2007) A charge pair interaction between Arg282 in transmembrane segment 7 and Asp341 in transmembrane segment 8 of hPepT1. Pharm Res 24(1):66\u201372. https:\/\/doi.org\/10.1007\/s11095-006-9119-x. Epub 2006 Sep 29. PMID: 17009102","journal-title":"Pharm Res"},{"issue":"12","key":"11710_CR38","doi-asserted-by":"publisher","first-page":"1911","DOI":"10.1023\/b:pham.0000008036.05892.e9","volume":"20","author":"T Uchiyama","year":"2003","unstructured":"Uchiyama T, Kulkarni AA, Davies DL, Lee VH (2003) Biophysical evidence for His57 as a proton-binding site in the mammalian intestinal transporter hPepT1. Pharm Res 20(12):1911\u20131916. https:\/\/doi.org\/10.1023\/b:pham.0000008036.05892.e9","journal-title":"Pharm Res"},{"issue":"12","key":"11710_CR39","doi-asserted-by":"publisher","first-page":"3636","DOI":"10.1021\/jm0511029","volume":"49","author":"BS Vig","year":"2006","unstructured":"Vig BS, Stouch TR, Timoszyk JK, Quan Y, Wall DA, Smith RL, Faria TN (2006) Human PEPT1 pharmacophore distinguishes between dipeptide transport and binding. J Med Chem 49(12):3636\u20133644. https:\/\/doi.org\/10.1021\/jm0511029","journal-title":"J Med Chem"},{"key":"11710_CR40","doi-asserted-by":"publisher","unstructured":"Abramson, J., Adler, J., Dunger, J., Evans, R., Green, T., Pritzel, A., ... & Jumper, J. M. (2024). Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature, 630(8016), 493-500. https:\/\/doi.org\/10.1038\/s41586-024-07487-w","DOI":"10.1038\/s41586-024-07487-w"},{"key":"11710_CR41","doi-asserted-by":"publisher","unstructured":"Grosdidier A, Zoete V, Michielin O (2011) SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic acids research, 39(Web Server issue). W270\u2013W277. https:\/\/doi.org\/10.1093\/nar\/gkr366","DOI":"10.1093\/nar\/gkr366"},{"key":"11710_CR42","doi-asserted-by":"publisher","first-page":"W324","DOI":"10.1093\/nar\/gkae300","volume":"52","author":"M Bugnon","year":"2024","unstructured":"Bugnon M, R\u00f6hrig UF, Goullieux M, Perez MAS, Daina A, Michielin O, Zoete V (2024) SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina. Nucleic Acids Res 52:W324\u2013W332. https:\/\/doi.org\/10.1093\/nar\/gkae300","journal-title":"Nucleic Acids Res"},{"key":"11710_CR43","doi-asserted-by":"publisher","unstructured":"Karag\u00f6l T, Karag\u00f6l A (2024) Benchmarking GROMACS on Optimized Colab Processors and the Flexibility of Cloud Computing for Molecular Dynamics. bioRxiv. 2024\u20132011. https:\/\/doi.org\/10.1101\/2024.11.14.623563","DOI":"10.1101\/2024.11.14.623563"},{"issue":"27","key":"11710_CR44","doi-asserted-by":"publisher","first-page":"1997","DOI":"10.1002\/jcc.23702","volume":"35","author":"EL Wu","year":"2014","unstructured":"Wu EL, Cheng X, Jo S, Rui H, Song KC, D\u00e1vila-Contreras EM, Qi Y, Lee J, Monje-Galvan V, Venable RM, Klauda JB, Im W (2014) CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. J Comput Chem 35(27):1997\u20132004. https:\/\/doi.org\/10.1002\/jcc.23702","journal-title":"J Comput Chem"},{"issue":"11","key":"11710_CR45","doi-asserted-by":"publisher","first-page":"1859","DOI":"10.1002\/jcc.20945","volume":"29","author":"S Jo","year":"2008","unstructured":"Jo S, Kim T, Iyer VG, Im W (2008) CHARMM-GUI: a web\u2010based graphical user interface for CHARMM. J Comput Chem 29(11):1859\u20131865. https:\/\/doi.org\/10.1002\/jcc.20945","journal-title":"J Comput Chem"},{"issue":"1","key":"11710_CR46","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1016\/j.bpj.2009.04.013","volume":"97","author":"S Jo","year":"2009","unstructured":"Jo S, Lim JB, Klauda JB, Im W (2009) CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. Biophys J 97(1):50\u201358. https:\/\/doi.org\/10.1016\/j.bpj.2009.04.013","journal-title":"Biophys J"},{"key":"11710_CR47","doi-asserted-by":"publisher","unstructured":"Lomize MA, Pogozheva ID, Joo H, Mosberg HI, Lomize AL (2012) OPM database and PPM web server: resources for positioning of proteins in membranes. Nucleic Acids Res. https:\/\/doi.org\/10.1093\/nar\/gkr703","DOI":"10.1093\/nar\/gkr703"},{"issue":"1","key":"11710_CR48","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1038\/nmeth.4067","volume":"14","author":"J Huang","year":"2017","unstructured":"Huang J, Rauscher S, Nawrocki G, Ran T, Feig M, De Groot BL, Grubm\u00fcller H, MacKerell AD Jr (2017) CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nat Methods 14(1):71\u201373. https:\/\/doi.org\/10.1038\/nmeth.4067","journal-title":"Nat Methods"},{"key":"11710_CR49","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","volume":"1","author":"MJ Abraham","year":"2015","unstructured":"Abraham MJ, Murtola T, Schulz R, P\u00e1ll S, Smith JC, Hess B, Lindahl E (2015) GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1:19\u201325. https:\/\/doi.org\/10.1016\/j.softx.2015.06.001","journal-title":"SoftwareX"},{"issue":"3","key":"11710_CR50","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1002\/jcc.540160303","volume":"16","author":"F Eisenhaber","year":"1995","unstructured":"Eisenhaber F, Lijnzaad P, Argos P, Sander C, Scharf M (1995) The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies. J Comput Chem 16(3):273\u2013284. https:\/\/doi.org\/10.1002\/jcc.540160303","journal-title":"J Comput Chem"},{"issue":"11","key":"11710_CR51","doi-asserted-by":"publisher","first-page":"e4792","DOI":"10.1002\/pro.4792","volume":"32","author":"EC Meng","year":"2023","unstructured":"Meng EC, Goddard TD, Pettersen EF, Couch GS, Pearson ZJ, Morris JH, Ferrin TE (2023) UCSF ChimeraX: Tools for structure building and analysis. Protein Sci 32(11):e4792. https:\/\/doi.org\/10.1002\/pro.4792","journal-title":"Protein Sci"},{"key":"11710_CR52","first-page":"29287","volume":"34","author":"J Meier","year":"2021","unstructured":"Meier J, Rao R, Verkuil R, Liu J, Sercu T, Rives A (2021) Language models enable zero-shot prediction of the effects of mutations on protein function. Adv Neural Inf Process Syst 34:29287\u201329303","journal-title":"Adv Neural Inf Process Syst"},{"key":"11710_CR53","doi-asserted-by":"crossref","unstructured":"Notin P, Kollasch AW, Ritter D, van Niekerk L, Paul S, Spinner H, Rollins N, Shaw A, Orenbuch R, Weitzman R, Frazer J, Dias M, Franceschi D, Gal Y, Marks DS (2023) ProteinGym: Large-scale benchmarks for protein fitness prediction and design. Adv Neural Inf Process Syst. 36:64331-64379","DOI":"10.52202\/075280-2810"}],"container-title":["Molecular Diversity"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11030-026-11710-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s11030-026-11710-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11030-026-11710-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T02:02:35Z","timestamp":1790388155000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s11030-026-11710-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,25]]},"references-count":53,"alternative-id":["11710"],"URL":"https:\/\/doi.org\/10.1007\/s11030-026-11710-3","relation":{},"ISSN":["1573-501X"],"issn-type":[{"value":"1573-501X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,25]]},"assertion":[{"value":"23 March 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 August 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 September 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Ethics approval was not required for this computational study as it did not involve animal subjects, human participants, and identifiable data.","order":1,"name":"Ethics","label":"Ethical approval","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable. This computational study did not involve human participants.","order":2,"name":"Ethics","label":"consent to participate","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable. This computational study did not involve human participants.","order":3,"name":"Ethics","label":"Consent for publication","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","label":"Conflict of interest","group":{"name":"EthicsHeading","label":"Declarations"}}]}}