{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,7]],"date-time":"2024-09-07T23:28:50Z","timestamp":1725751730462},"publisher-location":"Cham","reference-count":27,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783319026237"},{"type":"electronic","value":"9783319026244"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013]]},"DOI":"10.1007\/978-3-319-02624-4_9","type":"book-chapter","created":{"date-parts":[[2013,10,12]],"date-time":"2013-10-12T02:21:00Z","timestamp":1381544460000},"page":"94-103","source":"Crossref","is-referenced-by-count":2,"title":["Influence of Scaffold Stability and Electrostatics on Top7-Based Engineered Helical HIV-1 Epitopes"],"prefix":"10.1007","author":[{"given":"Isabelle F. T.","family":"Viana","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rafael","family":"Dhalia","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marco A.","family":"Krieger","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ernesto T. A.","family":"Marques","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roberto D.","family":"Lins","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"9_CR1","doi-asserted-by":"publisher","first-page":"11790","DOI":"10.1039\/c3ra41562g","volume":"3","author":"I.F.T. Viana","year":"2013","unstructured":"Viana, I.F.T., Soares, T.A., Lima, L.F.O., Marques, E.T.A., Krieger, M., Dhalia, R., Lins, R.D.: De Novo Design of Immunoreactive Conformation-specific HIV-1 Epitopes based on Top7 Scaffold. RSC Advances\u00a03, 11790\u201311800 (2013)","journal-title":"RSC Advances"},{"key":"9_CR2","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1006\/meth.1999.0926","volume":"20","author":"D.E. Leckband","year":"2000","unstructured":"Leckband, D.E., Kuhl, T.L., Wang, H.K., Muller, W., Herron, J., Ringsdorf, H.: Force probe measurements of antibody-antigen interactions. Methods\u00a020, 329\u2013340 (2000)","journal-title":"Methods"},{"key":"9_CR3","volume-title":"Immunobiology: The Immune System in Health and Disease","author":"C.A. Janeway Jr.","year":"2001","unstructured":"Janeway Jr., C.A., Travers, P., Walport, M., et al.: Immunobiology: The Immune System in Health and Disease. Garland Science, New York (2001)"},{"key":"9_CR4","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1002\/pro.5560060106","volume":"6","author":"C.J. Tsai","year":"1997","unstructured":"Tsai, C.J., Lin, S.L., Wolfson, H.J., Nussinov, R.: Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect. Protein Sci.\u00a06, 53\u201364 (1997)","journal-title":"Protein Sci."},{"key":"9_CR5","doi-asserted-by":"publisher","first-page":"570","DOI":"10.1006\/jmbi.1997.0987","volume":"268","author":"A.J. McCoy","year":"1997","unstructured":"McCoy, A.J., Chandana Epa, V., Colman, P.M.: Electrostatic complementarity at protein\/protein interfaces. Journal of Molecular Biology\u00a0268, 570\u2013584 (1997)","journal-title":"Journal of Molecular Biology"},{"key":"9_CR6","doi-asserted-by":"publisher","first-page":"2946","DOI":"10.1016\/S0006-3495(02)75302-2","volume":"83","author":"N. Sinha","year":"2002","unstructured":"Sinha, N., Mohan, S., Lipschultz, C.A., Smith-Gill, S.J.: Differences in electrostatic properties at antibody-antigen binding sites: implications for specificity and cross-reactivity. Biophys. J.\u00a083, 2946\u20132968 (2002)","journal-title":"Biophys. J."},{"key":"9_CR7","doi-asserted-by":"publisher","first-page":"1921","DOI":"10.1016\/j.bpj.2009.12.4332","volume":"98","author":"S. Fiorucci","year":"2010","unstructured":"Fiorucci, S., Zacharias, M.: Prediction of protein-protein interaction sites using electrostatic desolvation profiles. Biophys. J.\u00a098, 1921\u20131930 (2010)","journal-title":"Biophys. J."},{"key":"9_CR8","doi-asserted-by":"crossref","first-page":"W522","DOI":"10.1093\/nar\/gkm276","volume":"35","author":"T.J. Dolinsky","year":"2007","unstructured":"Dolinsky, T.J., Czodrowski, P., Li, H., Nielsen, J.E., Jensen, J.H., Klebe, G., Baker, N.A.: PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Research\u00a035, W522\u2013W525 (2007)","journal-title":"Nucleic Acids Research"},{"key":"9_CR9","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1186\/1472-6807-11-6","volume":"11","author":"M. Rostkowski","year":"2011","unstructured":"Rostkowski, M., Olsson, M.H.M., Sondergaard, C.R., Jensen, J.H.: Graphical analysis of pH-dependent properties of proteins predicted using PROPKA. BMC Structural Biology\u00a011, 6 (2011)","journal-title":"BMC Structural Biology"},{"key":"9_CR10","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1002\/jcc.540110315","volume":"11","author":"M.E. Davis","year":"1990","unstructured":"Davis, M.E., McCammon, J.A.: Calculating Electrostatic Forces from Grid-Calculated Potentials. Journal of Computational Chemistry\u00a011, 401\u2013409 (1990)","journal-title":"Journal of Computational Chemistry"},{"key":"9_CR11","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1002\/jcc.540120405","volume":"12","author":"A. Nicholls","year":"1991","unstructured":"Nicholls, A., Honig, B.: A Rapid Finite-Difference Algorithm, Utilizing Successive over-Relaxation to Solve the Poisson-Boltzmann Equation. Journal of Computational Chemistry\u00a012, 435\u2013445 (1991)","journal-title":"Journal of Computational Chemistry"},{"key":"9_CR12","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1002\/ijch.199400020","volume":"34","author":"J. Antosiewicz","year":"1994","unstructured":"Antosiewicz, J., Gilson, M.K., McCammon, J.A.: Acetylcholinesterase - Effects of Ionic-Strength and Dimerization on the Rate Constants. Israel Journal of Chemistry\u00a034, 151\u2013158 (1994)","journal-title":"Israel Journal of Chemistry"},{"key":"9_CR13","doi-asserted-by":"publisher","first-page":"10037","DOI":"10.1073\/pnas.181342398","volume":"98","author":"N.A. Baker","year":"2001","unstructured":"Baker, N.A., Sept, D., Joseph, S., Holst, M.J., McCammon, J.A.: Electrostatics of nanosystems: Application to microtubules and the ribosome. Proceedings of the National Academy of Sciences of the United States of America\u00a098, 10037\u201310041 (2001)","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"9_CR14","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","volume":"14","author":"W. Humphrey","year":"1996","unstructured":"Humphrey, W., Dalke, A., Schulten, K.: VMD: visual molecular dynamics. J. Mol. Graph.\u00a014, 33\u201338 (1996)","journal-title":"J. Mol. Graph."},{"key":"9_CR15","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1093\/bioinformatics\/btp016","volume":"25","author":"B.M. Bulheller","year":"2009","unstructured":"Bulheller, B.M., Hirst, J.D.: DichroCalc-circular and linear dichroism online. Bioinformatics\u00a025, 539\u2013540 (2009)","journal-title":"Bioinformatics"},{"key":"9_CR16","doi-asserted-by":"publisher","first-page":"2577","DOI":"10.1002\/bip.360221211","volume":"22","author":"W. Kabsch","year":"1983","unstructured":"Kabsch, W., Sander, C.: Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers\u00a022, 2577\u20132637 (1983)","journal-title":"Biopolymers"},{"key":"9_CR17","doi-asserted-by":"publisher","first-page":"1627","DOI":"10.1021\/ac60214a047","volume":"36","author":"A. Savitzky","year":"1964","unstructured":"Savitzky, A., Golay, M.J.E.: Smoothing and Differentiation of Data by Simplified Least Squares Procedures. Anal. Chem.\u00a036, 1627\u20131639 (1964)","journal-title":"Anal. Chem."},{"key":"9_CR18","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1093\/protein\/gzp007","volume":"22","author":"C.B. Boschek","year":"2009","unstructured":"Boschek, C.B., Apiyo, D.O., Soares, T.A., Engelmann, H.E., Pefaur, N.B., Straatsma, T.P., Baird, C.L.: Engineering an ultra-stable affinity reagent based on Top7. Protein Engineering, Design & Selection\u00a022, 325\u2013332 (2009)","journal-title":"Protein Engineering, Design & Selection"},{"key":"9_CR19","doi-asserted-by":"publisher","first-page":"755","DOI":"10.1016\/j.jmgm.2010.01.013","volume":"28","author":"T.A. Soares","year":"2010","unstructured":"Soares, T.A., Boschek, C.B., Apiyo, D., Baird, C., Straatsma, T.P.: Molecular basis of the structural stability of a Top7-based scaffold at extreme pH and temperature conditions. J. Mol. Graph. Model.\u00a028, 755\u2013765 (2010)","journal-title":"J. Mol. Graph. Model."},{"key":"9_CR20","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1016\/S0301-4622(02)00187-4","volume":"101-102","author":"R.W. Woody","year":"2002","unstructured":"Woody, R.W., Koslowski, A.: Recent developments in the electronic spectroscopy of amides and alpha-helical polypeptides. Biophys. Chem.\u00a0101-102, 535\u2013551 (2002)","journal-title":"Biophys. Chem."},{"key":"9_CR21","first-page":"164","volume":"3","author":"D.H. Correa","year":"2009","unstructured":"Correa, D.H., Ramos, C.H.I.: The use of circular dichroism spectroscopy to study protein folding, form and function. African J. Biochem. Res.\u00a03, 164\u2013173 (2009)","journal-title":"African J. Biochem. Res."},{"key":"9_CR22","doi-asserted-by":"publisher","first-page":"601","DOI":"10.2174\/1389203023380431","volume":"3","author":"N. Sinha","year":"2002","unstructured":"Sinha, N., Smith-Gill, S.J.: Electrostatics in protein binding and function. Curr. Protein Pept. Sci.\u00a03, 601\u2013614 (2002)","journal-title":"Curr. Protein Pept. Sci."},{"key":"9_CR23","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1073\/pnas.93.1.13","volume":"93","author":"S. Jones","year":"1996","unstructured":"Jones, S., Thornton, J.M.: Principles of protein-protein interactions. Proc. Natl. Acad. Sci. U. S. A.\u00a093, 13\u201320 (1996)","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"9_CR24","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1002\/prot.340210105","volume":"21","author":"J. Janin","year":"1995","unstructured":"Janin, J.: Elusive affinities. Proteins\u00a021, 30\u201339 (1995)","journal-title":"Proteins"},{"key":"9_CR25","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1006\/jmbi.1997.1203","volume":"272","author":"H.A. Gabb","year":"1997","unstructured":"Gabb, H.A., Jackson, R.M., Sternberg, M.J.E.: Modelling protein docking using shape complementarity, electrostatics and biochemical information. Journal of Molecular Biology\u00a0272, 106\u2013120 (1997)","journal-title":"Journal of Molecular Biology"},{"key":"9_CR26","doi-asserted-by":"publisher","first-page":"2946","DOI":"10.1016\/S0006-3495(02)75302-2","volume":"83","author":"N. Sinha","year":"2002","unstructured":"Sinha, N., Mohan, S., Lipschultz, C.A., Smith-Gill, S.J.: Differences in Electrostatic Properties at Antibody-Antigen Binding Sites: Implications for Specificity and Cross-Reactivity. Biophysical Journal\u00a083, 2946\u20132968 (2002)","journal-title":"Biophysical Journal"},{"key":"9_CR27","doi-asserted-by":"publisher","first-page":"5532","DOI":"10.1073\/pnas.86.14.5532","volume":"86","author":"N.C. Chien","year":"1989","unstructured":"Chien, N.C., Roberts, V.A., Giusti, A.M., Scharff, M.D., Getzoff, E.D.: Significant structural and functional change of an antigen-binding site by a distant amino acid substitution: proposal of a structural mechanism. Proc. Natl. Acad. Sci. U. S. A.\u00a086, 5532\u20135536 (1989)","journal-title":"Proc. Natl. Acad. Sci. U. S. A."}],"container-title":["Lecture Notes in Computer Science","Advances in Bioinformatics and Computational Biology"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-02624-4_9","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,23]],"date-time":"2019-05-23T06:33:57Z","timestamp":1558593237000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-319-02624-4_9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013]]},"ISBN":["9783319026237","9783319026244"],"references-count":27,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-02624-4_9","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2013]]}}}