{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T06:18:30Z","timestamp":1775801910316,"version":"3.50.1"},"reference-count":75,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2019,3,13]],"date-time":"2019-03-13T00:00:00Z","timestamp":1552435200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100007048","name":"Mayo Foundation for Medical Education and Research","doi-asserted-by":"publisher","award":["N\/A"],"award-info":[{"award-number":["N\/A"]}],"id":[{"id":"10.13039\/100007048","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Chlorotoxin (CTX) is a 36\u2013amino acid peptide with eight Cys residues that forms four disulfide bonds. It has high affinity for the glioma-specific chloride channel and matrix metalloprotease-2. Structural and binding properties of CTX analogs with various Cys residue substitutions with l-\u03b1-aminobutyric acid (Abu) have been previously reported. Using 4.2 \u00b5s molecular dynamics, we compared the conformational and essential space sampling of CTX and analogs with selective substitution of the Cys residues and associated disulfide bonds with either Abu or Ser. The native and substituted peptides maintained a high degree of \u03b1-helix propensity from residues 8 through 21, with the exception of substitution of the Cys5\u2013Cys28 residues with Ser and the Cys16\u2013Cys33 residues with Abu. In agreement with previous circular dichroism spectropolarimetry results, the C-terminal \u03b2-sheet content varied less from residues 25 through 29 and 32 through 36 and was well conserved in most analogs. The Cys16\u2013Cys33 and Cys20\u2013Cys35 disulfide-bonded residues appear to be required to maintain the \u03b1\u03b2 motif of CTX. Selective substitution with the hydrophilic Ser, may mitigate the destabilizing effect of Cys16\u2013Cys33 substitution through the formation of an inter residue H-bond from Ser16:O\u03b3H to Ser33:O\u03b3H bridged by a water molecule. All peptides shared considerable sampled conformational space, which explains the retained receptor binding of the non-native analogs.<\/jats:p>","DOI":"10.3390\/ijms20061261","type":"journal-article","created":{"date-parts":[[2019,3,14]],"date-time":"2019-03-14T04:15:29Z","timestamp":1552536929000},"page":"1261","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Effects of Selective Substitution of Cysteine Residues on the Conformational Properties of Chlorotoxin Explored by Molecular Dynamics Simulations"],"prefix":"10.3390","volume":"20","author":[{"given":"Andrew J.","family":"Gregory","sequence":"first","affiliation":[{"name":"Department of Neurosurgery, Mayo Clinic Health System-Franciscan Healthcare in La Crosse, La Crosse, WI 54601, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leah","family":"Voit-Ostricki","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Mayo Clinic Health System-Franciscan Healthcare in La Crosse, La Crosse, WI 54601, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S\u00e1ndor","family":"Lovas","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5011-487X","authenticated-orcid":false,"given":"Charles R.","family":"Watts","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Mayo Clinic Health System-Franciscan Healthcare in La Crosse, La Crosse, WI 54601, USA"},{"name":"Department of Neurologic Surgery, Mayo Clinic, Rochester, MN 55905, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2019,3,13]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1016\/0041-0101(91)90128-E","article-title":"Chloride Channel Inhibition by the venom of the scorpion Leiurus Quinquestriatus","volume":"29","author":"DeBin","year":"1991","journal-title":"Toxicon"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"C361","DOI":"10.1152\/ajpcell.1993.264.2.C361","article-title":"Purification and characterization of chlorotoxin, a chloride channel ligand from the venom of the scorpion","volume":"264","author":"DeBin","year":"1993","journal-title":"Am. J. Physiol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"5572","DOI":"10.1523\/JNEUROSCI.23-13-05572.2003","article-title":"Expression of voltage-gated chloride channels in human glioma cells","volume":"23","author":"Olsen","year":"2003","journal-title":"J. Neurosci."},{"key":"ref_4","first-page":"4871","article-title":"Use of chlorotoxin for targeting of primary brain tumors","volume":"58","author":"Soroceanu","year":"1998","journal-title":"Cancer Res."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1002\/glia.10083","article-title":"Chlorotoxin, a scorpion-derived peptide, specifically binds to gliomas and tumors of neuroectodermal origin","volume":"39","author":"Lyons","year":"2002","journal-title":"Glia"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1517\/17425247.4.2.175","article-title":"Targeted delivery of antitumoral therapy to glioma and other malignancies with synthetic chlorotoxin (TM-601)","volume":"4","author":"Mamelak","year":"2007","journal-title":"Expert. Opin. Drug Deliv."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1002\/smll.200800646","article-title":"Inhibition of tumor-cell invasion with chlorotoxin-bound superparamagnetic nanoparticles","volume":"5","author":"Veiseh","year":"2009","journal-title":"Small"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"6882","DOI":"10.1158\/0008-5472.CAN-06-3948","article-title":"Tumor paint: A chlorotoxin:Cy5.5 bioconjugate for intraoperative visualization of cancer foci","volume":"67","author":"Veiseh","year":"2007","journal-title":"Cancer Res."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"782","DOI":"10.1021\/jm101018r","article-title":"Chemical re-engineering of chlorotoxin improves bioconjugation properties for tumor imaging and targeted therapy","volume":"54","author":"Akcan","year":"2011","journal-title":"J. Med. Chem."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"9807","DOI":"10.1021\/jm4016119","article-title":"Correction to Chemical Re-engineering of Chlorotoxin Improves Bioconjugation Properties for Tumor Imaging and Targeted Therapy","volume":"56","author":"Akcan","year":"2013","journal-title":"J. Med. Chem."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1016\/0041-0101(85)90114-X","article-title":"Characterization of ten proteins from the venom of the Moroccan scorpion Androctonus mauretanicus mauretanicus, six of which are toxic to the mouse","volume":"23","author":"Rosso","year":"1985","journal-title":"Toxicon"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1016\/S1095-6433(98)10140-X","article-title":"Purification and primary structure of low molecular mass peptides from scorpion (Buthus sindicus) venom","volume":"121","author":"Ali","year":"1998","journal-title":"Comput. Biochem. Physiol. A Mol. Integr. Physiol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1046\/j.1432-1327.1999.00625.x","article-title":"Scorpion toxins specific for Na+-channels","volume":"264","author":"Possani","year":"1999","journal-title":"Eur. J. Biochem."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1016\/S0300-9084(00)01167-6","article-title":"Peptides and genes coding for scorpion toxins that affect ion-channels","volume":"82","author":"Possani","year":"2000","journal-title":"Biochimie"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1146\/annurev.genom.9.081307.164356","article-title":"The toxicogenomic multiverse: Convergent recruitment of proteins into animal venoms","volume":"10","author":"Fry","year":"2009","journal-title":"Annu. Rev. Genomics Hum. Genet."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1521","DOI":"10.1126\/science.1720574","article-title":"Refined structure of charybdotoxin: Common motifs in scorpion toxins and insect defensins","volume":"254","author":"Bontems","year":"1991","journal-title":"Science"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1007\/BF01875319","article-title":"Two-dimensional 1H NMR study of recombinant insect defensin A in water: Resonance assignments, secondary structure and global folding","volume":"2","author":"Bonmatin","year":"1992","journal-title":"J. Biomol. NMR"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1016\/S0969-2126(01)00177-0","article-title":"Refined three-dimensional solution structure of insect defensin A","volume":"3","author":"Cornet","year":"1995","journal-title":"Structure"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"715","DOI":"10.1021\/bi00053a041","article-title":"Solution structure of gamma 1-H and gamma 1-P thionins from barley and wheat endosperm determined by 1H-NMR: A structural motif common to toxic arthropod proteins","volume":"32","author":"Bruix","year":"1993","journal-title":"Biochemistry"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/S0041-0101(00)00160-4","article-title":"The cystine knot motif in toxins and implications for drug design","volume":"39","author":"Craik","year":"2001","journal-title":"Toxicon"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Ali, S.A., Alam, M., Abbasi, A., Undheim, E.A.B., Fry, B.G., Kalbacher, H., and Voelter, W. (2016). Structure-Activity Relationship of Chlorotoxin-Like Peptides. Toxins, 8.","DOI":"10.3390\/toxins8020036"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1042\/bj20031860","article-title":"Diversity of folds in animal toxins acting on ion channels","volume":"378","author":"Mouhat","year":"2004","journal-title":"Biochem. J."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1016\/j.biotechadv.2004.09.002","article-title":"Formation of disulfide bonds in proteins and peptides","volume":"23","author":"Bulaj","year":"2005","journal-title":"Biotechnol. Adv."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"10641","DOI":"10.1021\/bi960533d","article-title":"Synthesis and characterization of leiurotoxin I analogs lacking one disulfide bridge: Evidence that disulfide pairing 3\u201321 is not required for full toxin activity","volume":"35","author":"Sabatier","year":"1996","journal-title":"Biochemistry"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1292","DOI":"10.1021\/bi9721086","article-title":"Consequence of the removal of evolutionary conserved disulfide bridges on the structure and function of charybdotoxin and evidence that particular cysteine spacings govern specific disulfide bond formation","volume":"37","author":"Drakopoulou","year":"1998","journal-title":"Biochemistry"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"11488","DOI":"10.1021\/bi026136m","article-title":"Role of disulfide bonds in folding and activity of leiurotoxin I: Just two disulfides suffice","volume":"41","author":"Zhu","year":"2002","journal-title":"Biochemistry"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"3760","DOI":"10.1021\/bi962720h","article-title":"NMR solution structure of a two-disulfide derivative of charybdotoxin: Structural evidence for conservation of scorpion toxin alpha\/beta motif and its hydrophobic side chain packing","volume":"36","author":"Song","year":"1997","journal-title":"Biochemistry"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1002\/bip.22748","article-title":"Chlorotoxin: Structure, activity, and potential uses in cancer therapy","volume":"106","author":"Ojeda","year":"2016","journal-title":"Biopolymers"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1617","DOI":"10.4155\/fmc.14.93","article-title":"The role of disulfide bonds in structure and activity of chlorotoxin","volume":"6","author":"Ojeda","year":"2014","journal-title":"Future Med. Chem."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1021\/bi00001a003","article-title":"NMR sequential assignments and solution structure of chlorotoxin, a small scorpion toxin that blocks chloride channels","volume":"34","author":"Lippens","year":"1995","journal-title":"Biochemistry"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.1002\/bip.360221211","article-title":"Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features","volume":"22","author":"Kabsch","year":"1983","journal-title":"Biopolymers"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1002\/prot.340230412","article-title":"Knowledge-based protein secondary structure assignment","volume":"23","author":"Frishman","year":"1995","journal-title":"Proteins"},{"key":"ref_33","unstructured":"Epton, R. (1994). Charybdotoxin Analogs Missing One Disulfide Bridge. Innovation and Perspectives in Solid Phase Synthesis: Peptides, Proteins and Nucleic Acids: Biological and Biomedical Applications, Proceedings of the Third International Symposium, Oxford, England, UK, 31 August\u20134 September 1993, Mayflower Worldwide."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1038\/nmeth.4067","article-title":"CHARMM36m: An improved force field for folded and intrinsically disordered proteins","volume":"14","author":"Huang","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"3257","DOI":"10.1021\/ct300400x","article-title":"Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone phi, psi and side-chain chi(1) and chi(2) dihedral angles","volume":"8","author":"Best","year":"2012","journal-title":"J. Chem. Theory Comput."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1400","DOI":"10.1002\/jcc.20065","article-title":"Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations","volume":"25","author":"Mackerell","year":"2004","journal-title":"J. Comput. Chem."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"3586","DOI":"10.1021\/jp973084f","article-title":"All-atom empirical potential for molecular modeling and dynamics studies of proteins","volume":"102","author":"MacKerell","year":"1998","journal-title":"J. Phys. Chem. B"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1002\/jcc.21367","article-title":"CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields","volume":"31","author":"Vanommeslaeghe","year":"2009","journal-title":"J. Comput. Chem."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers","volume":"1\u20132","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Markidis, S., and Laure, E. (2015). Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS. Solving Software Challenges for Exascale: International Conference on Exascale Applications and Software Proceedings of the EASC2014, Stockholm, Sweden, 2\u20133 April 2014, Springer International Publishing.","DOI":"10.1007\/978-3-319-15976-8"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1021\/ct700301q","article-title":"GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation","volume":"4","author":"Hess","year":"2008","journal-title":"J. Chem. Theory Comput."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1701","DOI":"10.1002\/jcc.20291","article-title":"GROMACS: Fast, flexible, and free","volume":"26","author":"Lindahl","year":"2005","journal-title":"J. Comput. Chem."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1007\/s008940100045","article-title":"GROMACS 3.0: A package for molecular simulation and trajectory analysis","volume":"7","author":"Lindahl","year":"2001","journal-title":"J. Mol. Mod."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/0010-4655(95)00042-E","article-title":"GROMACS: A message-passing parallel molecular dynamics implementation","volume":"91","author":"Berendsen","year":"1995","journal-title":"Comput. Phys. Commun."},{"key":"ref_45","unstructured":"Abraham, M.J., van der Spoel, D., Lindahl, E., Hess, B., and the GROMACS Development Team (2017, June 01). GROMACS User Manual Version 5.1.2. Available online: http:\/\/www.gromacs.org."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1021\/ct900549r","article-title":"Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models","volume":"6","author":"Bjelkmar","year":"2010","journal-title":"J. Chem. Theory Comput."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"2981","DOI":"10.1093\/bioinformatics\/btu426","article-title":"YASARA View-molecular graphics for all devices\u2014from smartphones to workstations","volume":"30","author":"Krieger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"014101","DOI":"10.1063\/1.2408420","article-title":"Canonical sampling through velocity rescaling","volume":"126","author":"Bussi","year":"2007","journal-title":"J. Chem. Phys."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"3684","DOI":"10.1063\/1.448118","article-title":"Molecular dynamics with coupling to an external bath","volume":"81","author":"Berendsen","year":"1984","journal-title":"J. Chem. Phys."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H","article-title":"LINCS: A linear constraint solver for molecular simulations","volume":"18","author":"Hess","year":"1997","journal-title":"J. Comput. Chem."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1021\/ct700200b","article-title":"P-LINCS:\u2009 A Parallel Linear Constraint Solver for Molecular Simulation","volume":"4","author":"Hess","year":"2008","journal-title":"J. Chem. Theory Comput."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"8577","DOI":"10.1063\/1.470117","article-title":"A smooth particle mesh Ewald method","volume":"103","author":"Essmann","year":"1995","journal-title":"J. Chem. Phys."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"7182","DOI":"10.1063\/1.328693","article-title":"Polymorphic transitions in single crystals: A new molecular dynamics method","volume":"52","author":"Parrinello","year":"1981","journal-title":"J. Appl. Phys."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1006\/jmbi.1993.1438","article-title":"Determination of the disulfide bonding pattern in proteins by local and global analysis of nuclear magnetic resonance data. Application to flavoridin","volume":"232","author":"Klaus","year":"1993","journal-title":"J. Mol. Biol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1016\/0022-2836(71)90324-X","article-title":"The interpretation of protein structures: Estimation of static accessibility","volume":"55","author":"Lee","year":"1971","journal-title":"J. Mol. Biol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1483","DOI":"10.1016\/S0006-3495(92)81746-0","article-title":"Residue solvent accessibilities in the unfolded polypeptide chain","volume":"63","author":"Zielenkiewicz","year":"1992","journal-title":"Biophys. J."},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Tien, M.Z., Meyer, A.G., Sydykova, D.K., Spielman, S.J., and Wilke, C.O. (2013). Maximum allowed solvent accessibilities of residues in proteins. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0080635"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"7254","DOI":"10.1021\/jp4024469","article-title":"Free energy of solvated salt bridges: A simulation and experimental study","volume":"117","author":"White","year":"2013","journal-title":"J. Phys. Chem. B"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"1399","DOI":"10.1021\/ct501116v","article-title":"Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins","volume":"11","author":"Nguyen","year":"2015","journal-title":"J. Chem. Theory Comput."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1002\/prot.20310","article-title":"Energy landscape of a small peptide revealed by dihedral angle principal component analysis","volume":"58","author":"Mu","year":"2005","journal-title":"Proteins"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"244111","DOI":"10.1063\/1.2746330","article-title":"Dihedral angle principal component analysis of molecular dynamics simulations","volume":"126","author":"Altis","year":"2007","journal-title":"J. Chem. Phys."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v008.i11","article-title":"scatterplot3d\u2014An R Package for Visualizing Multivariate Data","volume":"8","author":"Ligges","year":"2003","journal-title":"J. Stat. Softw."},{"key":"ref_63","unstructured":"Akima, H., Gebhardt, A., Petzold, T., and Maechler, M. (2006, August 06). Akima: Interpolation of Irregularly and Regularly Spaced Data. Available online: https:\/\/cran.r-project.org\/web\/packages\/akima\/."},{"key":"ref_64","unstructured":"Sarkar, D., and Andrews, F. (2018, August 06). latticeExtra: Extra Graphical Utilities Based on Lattice. Available online: https:\/\/cran.r-project.org\/web\/packages\/latticeExtra\/."},{"key":"ref_65","unstructured":"R Core Team (2018, August 06). R: A language and environment for statistical computing. Available online: http:\/\/www.R-project.org\/."},{"key":"ref_66","unstructured":"Maechler, M., Rousseeuw, P., Struyf, A., Hubert, M., Hornik, K., Studer, M., Roudier, P., Gonzalez, J., and Kozlowski, K. (2018, August 06). Cluster: Methods for Cluster Analysis. Available online: https:\/\/cran.r-project.org\/web\/packages\/cluster\/."},{"key":"ref_67","unstructured":"Tan, P.-N., Steinbach, M., and Kumar, V. (2005). Cluster Analysis: Basic Concepts and Algorithms. Introduction to Data Mining, Pearson Addison Wesley. [2nd ed.]."},{"key":"ref_68","unstructured":"Tan, P.-N., Steinbach, M., and Kumar, V. (2005). Cluster Analysis: Additional Issues and Algorithms. Introduction to Data Mining, Pearson Addison Wesley. [2nd ed.]."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/0377-0427(87)90125-7","article-title":"Silhouettes: A graphical aid to the interpretation and validation of cluster analysis","volume":"20","author":"Rousseeuw","year":"1987","journal-title":"J. Comput. Appl. Math."},{"key":"ref_70","first-page":"44","article-title":"The Clustering Validity with Silhouette and Sum of Squared Errors","volume":"Volume 3","author":"Ehara","year":"2015","journal-title":"Proceedings of the 3rd International Conference on Industrial Application Engineering, Kitakyushu, Japan, 28\u201331 March 2015"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"6289","DOI":"10.1063\/1.1401821","article-title":"On the calculation of entropy from covariance matrices of the atomic fluctuations","volume":"115","author":"Andricioaei","year":"2001","journal-title":"J. Chem. Phys."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"031910","DOI":"10.1103\/PhysRevE.65.031910","article-title":"Convergence of sampling in protein simulations","volume":"65","author":"Hess","year":"2002","journal-title":"Phys. Rev. E Stat. Nonlin. Soft Matter Phys."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"448","DOI":"10.1002\/bip.20090","article-title":"Characterization of the conformational behavior of peptide Contryphan Vn: A theoretical study","volume":"74","author":"Paci","year":"2004","journal-title":"Biopolymers"},{"key":"ref_74","doi-asserted-by":"crossref","unstructured":"Martin-Garcia, F., Papaleo, E., Gomez-Puertas, P., Boomsma, W., and Lindorff-Larsen, K. (2015). Comparing molecular dynamics force fields in the essential subspace. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0121114"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"48621","DOI":"10.1039\/C4RA09897H","article-title":"New CHARMM force field parameters for dehydrated amino acid residues, the key to lantibiotic molecular dynamics simulations","volume":"4","author":"Turpin","year":"2014","journal-title":"RSC Adv."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/20\/6\/1261\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T12:38:22Z","timestamp":1760186302000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/20\/6\/1261"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,3,13]]},"references-count":75,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2019,3]]}},"alternative-id":["ijms20061261"],"URL":"https:\/\/doi.org\/10.3390\/ijms20061261","relation":{"has-preprint":[{"id-type":"doi","id":"10.20944\/preprints201812.0214.v1","asserted-by":"object"}]},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,3,13]]}}}