{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,4]],"date-time":"2025-10-04T07:36:15Z","timestamp":1759563375933},"reference-count":37,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2015,3,27]],"date-time":"2015-03-27T00:00:00Z","timestamp":1427414400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1186\/s12859-015-0528-x","type":"journal-article","created":{"date-parts":[[2015,3,27]],"date-time":"2015-03-27T16:42:35Z","timestamp":1427474555000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Understanding the molecular basis of EGFR kinase domain\/MIG-6 peptide recognition complex using computational analyses"],"prefix":"10.1186","volume":"16","author":[{"given":"Ninnutt","family":"Moonrin","sequence":"first","affiliation":[]},{"given":"Napat","family":"Songtawee","sequence":"additional","affiliation":[]},{"given":"Siriluk","family":"Rattanabunyong","sequence":"additional","affiliation":[]},{"given":"Surasuk","family":"Chunsrivirot","sequence":"additional","affiliation":[]},{"given":"Wanwimon","family":"Mokmak","sequence":"additional","affiliation":[]},{"given":"Sissades","family":"Tongsima","sequence":"additional","affiliation":[]},{"given":"Kiattawee","family":"Choowongkomon","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2015,3,27]]},"reference":[{"issue":"2","key":"528_CR1","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1016\/j.ceb.2008.12.010","volume":"21","author":"NE Hynes","year":"2009","unstructured":"Hynes NE, MacDonald G. ErbB receptors and signaling pathways in cancer. Curr Opin Cell Biol. 2009;21(2):177\u201384.","journal-title":"Curr Opin Cell Biol"},{"issue":"1","key":"528_CR2","first-page":"120","volume":"1766","author":"S Sebastian","year":"2006","unstructured":"Sebastian S, Settleman J, Reshkin SJ, Azzariti A, Bellizzi A, Paradiso A. The complexity of targeting EGFR signalling in cancer: from expression to turnover. Biochim Biophys Acta. 2006;1766(1):120\u201339.","journal-title":"Biochim Biophys Acta"},{"key":"528_CR3","doi-asserted-by":"crossref","first-page":"2855","DOI":"10.1038\/srep02855","volume":"3","author":"DD Wang","year":"2013","unstructured":"Wang DD, Zhou W, Yan H, Wong M, Lee V. Personalized prediction of EGFR mutation-induced drug resistance in lung cancer. Sci Rep. 2013;3:2855.","journal-title":"Sci Rep"},{"issue":"12","key":"528_CR4","doi-asserted-by":"publisher","first-page":"e82059","DOI":"10.1371\/journal.pone.0082059","volume":"8","author":"R Friedman","year":"2013","unstructured":"Friedman R. Drug resistance missense mutations in cancer are subject to evolutionary constraints. PLoS One. 2013;8(12):e82059.","journal-title":"PLoS One"},{"issue":"6","key":"528_CR5","doi-asserted-by":"publisher","first-page":"2070","DOI":"10.1073\/pnas.0709662105","volume":"105","author":"CH Yun","year":"2008","unstructured":"Yun CH, Mengwasser KE, Toms AV, Woo MS, Greulich H, Wong KK. The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP. Proc Natl Acad Sci U S A. 2008;105(6):2070\u20135.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"7170","key":"528_CR6","doi-asserted-by":"publisher","first-page":"741","DOI":"10.1038\/nature05998","volume":"450","author":"X Zhang","year":"2007","unstructured":"Zhang X, Pickin KA, Bose R, Jura N, Cole PA, Kuriyan J. Inhibition of the EGF receptor by binding of MIG6 to an activating kinase domain interface. Nature. 2007;450(7170):741\u20134.","journal-title":"Nature"},{"issue":"5","key":"528_CR7","doi-asserted-by":"publisher","first-page":"507","DOI":"10.4161\/cc.6.5.3928","volume":"6","author":"YW Zhang","year":"2007","unstructured":"Zhang YW, Vande Woude GF. Mig-6, signal transduction, stress response and cancer. Cell Cycle. 2007;6(5):507\u201313.","journal-title":"Cell Cycle"},{"issue":"2","key":"528_CR8","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1038\/sj.onc.1209790","volume":"26","author":"YW Zhang","year":"2007","unstructured":"Zhang YW, Staal B, Su Y, Swiatek P, Zhao P, Cao B, et al. Evidence that MIG-6 is a tumor-suppressor gene. Oncogene. 2007;26(2):269\u201376.","journal-title":"Oncogene"},{"issue":"8","key":"528_CR9","doi-asserted-by":"publisher","first-page":"2106","DOI":"10.1039\/c2mb25042j","volume":"8","author":"Y Yang","year":"2012","unstructured":"Yang Y, Liu H, Yao X. Understanding the molecular basis of MK2-p38alpha signaling complex assembly: insights into protein-protein interaction by molecular dynamics and free energy studies. Mol BioSyst. 2012;8(8):2106\u201318.","journal-title":"Mol BioSyst"},{"issue":"4","key":"528_CR10","doi-asserted-by":"publisher","first-page":"1421","DOI":"10.1007\/s00894-011-1159-4","volume":"18","author":"J Guo","year":"2012","unstructured":"Guo J, Wang X, Sun H, Liu H, Yao X. The molecular basis of IGF-II\/IGF2R recognition: a combined molecular dynamics simulation, free-energy calculation and computational alanine scanning study. J Mol Model. 2012;18(4):1421\u201330.","journal-title":"J Mol Model"},{"issue":"16","key":"528_CR11","doi-asserted-by":"publisher","first-page":"1668","DOI":"10.1002\/jcc.20290","volume":"26","author":"DA Case","year":"2005","unstructured":"Case DA, Cheatham 3rd TE, Darden T, Gohlke H, Luo R, Merz Jr KM, et al. The Amber biomolecular simulation programs. J Comput Chem. 2005;26(16):1668\u201388.","journal-title":"J Comput Chem"},{"issue":"2","key":"528_CR12","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1063\/1.445869","volume":"79","author":"WL Jorgensen","year":"1983","unstructured":"Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Physics. 1983;79(2):926\u201335.","journal-title":"J Chem Physics"},{"issue":"12","key":"528_CR13","doi-asserted-by":"publisher","first-page":"10089","DOI":"10.1063\/1.464397","volume":"98","author":"T Darden","year":"1993","unstructured":"Darden T, York D, Pedersen L. Particle mesh Ewald: an n\u22c5log (N) method for Ewald sums in large systems. J Chem Physics. 1993;98(12):10089\u201392.","journal-title":"J Chem Physics"},{"issue":"8","key":"528_CR14","doi-asserted-by":"publisher","first-page":"952","DOI":"10.1002\/jcc.540130805","volume":"13","author":"S Miyamoto","year":"1992","unstructured":"Miyamoto S, Kollman PA. Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comput Chem. 1992;13(8):952\u201362.","journal-title":"J Comput Chem"},{"issue":"12","key":"528_CR15","doi-asserted-by":"publisher","first-page":"889","DOI":"10.1021\/ar000033j","volume":"33","author":"PA Kollman","year":"2000","unstructured":"Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, et al. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res. 2000;33(12):889\u201397.","journal-title":"Acc Chem Res"},{"issue":"2","key":"528_CR16","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1002\/(SICI)1096-987X(19990130)20:2<217::AID-JCC4>3.0.CO;2-A","volume":"20","author":"J Weiser","year":"1999","unstructured":"Weiser J, Shenkin PS, Still WC. Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). J Comput Chem. 1999;20(2):217\u201330.","journal-title":"J Comput Chem"},{"issue":"1","key":"528_CR17","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1002\/prot.20275","volume":"58","author":"H Zhong","year":"2005","unstructured":"Zhong H, Carlson HA. Computational studies and peptidomimetic design for the human p53-MDM2 complex. Proteins. 2005;58(1):222\u201334.","journal-title":"Proteins"},{"issue":"5","key":"528_CR18","doi-asserted-by":"publisher","first-page":"813","DOI":"10.1016\/j.jmgm.2007.04.007","volume":"26","author":"T Li","year":"2008","unstructured":"Li T, Froeyen M, Herdewijn P. Computational alanine scanning and free energy decomposition for E. coli type I signal peptidase with lipopeptide inhibitor complex. J Mol Graph Model. 2008;26(5):813\u201323.","journal-title":"J Mol Graph Model"},{"issue":"1\u20132","key":"528_CR19","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1093\/protein\/gzq047","volume":"24","author":"RT Bradshaw","year":"2011","unstructured":"Bradshaw RT, Patel BH, Tate EW, Leatherbarrow RJ, Gould IR. Comparing experimental and computational alanine scanning techniques for probing a prototypical protein-protein interaction. Protein Eng Des Sel. 2011;24(1\u20132):197\u2013207.","journal-title":"Protein Eng Des Sel"},{"issue":"5","key":"528_CR20","doi-asserted-by":"publisher","first-page":"726","DOI":"10.1016\/j.jmgm.2010.12.005","volume":"29","author":"L Saiz-Urra","year":"2011","unstructured":"Saiz-Urra L, Cabrera MA, Froeyen M. Exploring the conformational changes of the ATP binding site of gyrase B from Escherichia coli complexed with different established inhibitors by using molecular dynamics simulation: protein-ligand interactions in the light of the alanine scanning and free energy decomposition methods. J Mol Graph Model. 2011;29(5):726\u201339.","journal-title":"J Mol Graph Model"},{"issue":"3","key":"528_CR21","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1016\/S1367-5931(00)00206-4","volume":"5","author":"KL Morrison","year":"2001","unstructured":"Morrison KL, Weiss GA. Combinatorial alanine-scanning. Curr Opin Chem Biol. 2001;5(3):302\u20137.","journal-title":"Curr Opin Chem Biol"},{"issue":"36","key":"528_CR22","doi-asserted-by":"publisher","first-page":"14220","DOI":"10.1021\/ja206074j","volume":"133","author":"BN Bullock","year":"2011","unstructured":"Bullock BN, Jochim AL, Arora PS. Assessing helical protein interfaces for inhibitor design. J Am Chem Soc. 2011;133(36):14220\u20133.","journal-title":"J Am Chem Soc"},{"issue":"36","key":"528_CR23","doi-asserted-by":"publisher","first-page":"8133","DOI":"10.1021\/ja990935j","volume":"121","author":"I Massova","year":"1999","unstructured":"Massova I, Kollman PA. Computational alanine scanning to probe protein\u2009\u2212\u2009protein interactions: a novel approach to evaluate binding free energies. J Am Chem Soc. 1999;121(36):8133\u201343.","journal-title":"J Am Chem Soc"},{"issue":"21","key":"528_CR24","doi-asserted-by":"publisher","first-page":"7045","DOI":"10.1021\/jp200075s","volume":"115","author":"SF Sousa","year":"2011","unstructured":"Sousa SF, Tamames B, Fernandes PA, Ramos MJ. Detailed atomistic analysis of the HIV-1 protease interface. J Phys Chem B. 2011;115(21):7045\u201357.","journal-title":"J Phys Chem B"},{"issue":"4","key":"528_CR25","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1002\/bip.20566","volume":"83","author":"LM Espinoza-Fonseca","year":"2006","unstructured":"Espinoza-Fonseca LM, Trujillo-Ferrara JG. Conformational changes of the p53-binding cleft of MDM2 revealed by molecular dynamics simulations. Biopolymers. 2006;83(4):365\u201373.","journal-title":"Biopolymers"},{"issue":"6","key":"528_CR26","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1016\/j.molcel.2009.04.034","volume":"34","author":"M Red Brewer","year":"2009","unstructured":"Red Brewer M, Choi SH, Alvarado D, Moravcevic K, Pozzi A, Lemmon MA, et al. The juxtamembrane region of the EGF receptor functions as an activation domain. Mol Cell. 2009;34(6):641\u201351.","journal-title":"Mol Cell"},{"issue":"1","key":"528_CR27","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1006\/jmbi.1995.0360","volume":"250","author":"AM Bonvin","year":"1995","unstructured":"Bonvin AM, Brunger AT. Conformational variability of solution nuclear magnetic resonance structures. J Mol Biol. 1995;250(1):80\u201393.","journal-title":"J Mol Biol"},{"issue":"2","key":"528_CR28","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1093\/protein\/8.2.127","volume":"8","author":"AC Wallace","year":"1995","unstructured":"Wallace AC, Laskowski RA, Thornton JM. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 1995;8(2):127\u201334.","journal-title":"Protein Eng"},{"issue":"25","key":"528_CR29","doi-asserted-by":"publisher","first-page":"15458","DOI":"10.1074\/jbc.273.25.15458","volume":"273","author":"GB McGaughey","year":"1998","unstructured":"McGaughey GB, Gagne M, Rappe AK. pi-Stacking interactions: alive and well in proteins. J Biol Chem. 1998;273(25):15458\u201363.","journal-title":"J Biol Chem"},{"issue":"7","key":"528_CR30","doi-asserted-by":"publisher","first-page":"e2524","DOI":"10.1371\/journal.pone.0002524","volume":"3","author":"A Stein","year":"2008","unstructured":"Stein A, Aloy P. Contextual specificity in peptide-mediated protein interactions. PLoS One. 2008;3(7):e2524.","journal-title":"PLoS One"},{"key":"528_CR31","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1016\/j.jmgm.2013.10.005","volume":"46","author":"RJ Niu","year":"2013","unstructured":"Niu RJ, Zheng QC, Zhang JL, Zhang HX. Molecular dynamics simulations studies and free energy analysis on inhibitors of MDM2-p53 interaction. J Mol Graph Model. 2013;46:132\u20139.","journal-title":"J Mol Graph Model"},{"issue":"1","key":"528_CR32","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1002\/jcc.1153","volume":"23","author":"S Huo","year":"2002","unstructured":"Huo S, Massova I, Kollman PA. Computational alanine scanning of the 1:1 human growth hormone-receptor complex. J Comput Chem. 2002;23(1):15\u201327.","journal-title":"J Comput Chem"},{"issue":"4","key":"528_CR33","doi-asserted-by":"publisher","first-page":"803","DOI":"10.1002\/prot.21396","volume":"68","author":"IS Moreira","year":"2007","unstructured":"Moreira IS, Fernandes PA, Ramos MJ. Hot spots\u2013a review of the protein-protein interface determinant amino-acid residues. Proteins. 2007;68(4):803\u201312.","journal-title":"Proteins"},{"issue":"5","key":"528_CR34","doi-asserted-by":"publisher","first-page":"958","DOI":"10.1110\/ps.8.5.958","volume":"8","author":"J Pons","year":"1999","unstructured":"Pons J, Rajpal A, Kirsch JF. Energetic analysis of an antigen\/antibody interface: alanine scanning mutagenesis and double mutant cycles on the HyHEL-10\/lysozyme interaction. Protein Sci. 1999;8(5):958\u201368.","journal-title":"Protein Sci"},{"issue":"2","key":"528_CR35","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1002\/prot.20417","volume":"59","author":"PB Crowley","year":"2005","unstructured":"Crowley PB, Golovin A. Cation-pi interactions in protein-protein interfaces. Proteins. 2005;59(2):231\u20139.","journal-title":"Proteins"},{"issue":"6","key":"528_CR36","doi-asserted-by":"publisher","first-page":"1137","DOI":"10.1016\/j.cell.2006.05.013","volume":"125","author":"X Zhang","year":"2006","unstructured":"Zhang X, Gureasko J, Shen K, Cole PA, Kuriyan J. An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor. Cell. 2006;125(6):1137\u201349.","journal-title":"Cell"},{"issue":"7","key":"528_CR37","doi-asserted-by":"publisher","first-page":"1293","DOI":"10.1016\/j.cell.2009.04.025","volume":"137","author":"N Jura","year":"2009","unstructured":"Jura N, Endres NF, Engel K, Deindl S, Das R, Lamers MH, et al. Mechanism for activation of the EGF receptor catalytic domain by the juxtamembrane segment. Cell. 2009;137(7):1293\u2013307.","journal-title":"Cell"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-015-0528-x\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-015-0528-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-015-0528-x","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-015-0528-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T09:37:16Z","timestamp":1630575436000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-015-0528-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,3,27]]},"references-count":37,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["528"],"URL":"https:\/\/doi.org\/10.1186\/s12859-015-0528-x","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,3,27]]},"assertion":[{"value":"8 September 2014","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 March 2015","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 March 2015","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"103"}}