{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T02:15:25Z","timestamp":1775873725032,"version":"3.50.1"},"reference-count":53,"publisher":"Springer Science and Business Media LLC","issue":"S5","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2014,5]]},"DOI":"10.1186\/1471-2105-15-s5-s1","type":"journal-article","created":{"date-parts":[[2014,5,6]],"date-time":"2014-05-06T11:02:59Z","timestamp":1399374179000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":30,"title":["MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories"],"prefix":"10.1186","volume":"15","author":[{"given":"Safwat","family":"Abdel-Azeim","sequence":"first","affiliation":[]},{"given":"Edrisse","family":"Chermak","sequence":"additional","affiliation":[]},{"given":"Anna","family":"Vangone","sequence":"additional","affiliation":[]},{"given":"Romina","family":"Oliva","sequence":"additional","affiliation":[]},{"given":"Luigi","family":"Cavallo","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2014,5,6]]},"reference":[{"key":"6369_CR1","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1101\/gad.14.9.1027","volume":"14","author":"T Pawson","year":"2000","unstructured":"Pawson T, Nash P: Protein-protein interactions define specificity in signal transduction. Genes Dev. 2000, 14: 1027-1047.","journal-title":"Genes Dev"},{"key":"6369_CR2","doi-asserted-by":"publisher","first-page":"857","DOI":"10.1016\/0959-440X(94)90267-4","volume":"4","author":"IA Wilson","year":"1994","unstructured":"Wilson IA, Stanfield RL: Antibody-antigen interactions: new structures and new conformational changes. Current opinion in structural biology. 1994, 4: 857-867. 10.1016\/0959-440X(94)90267-4.","journal-title":"Current opinion in structural biology"},{"key":"6369_CR3","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 JM: Principles of protein-protein interactions. Proceedings of the National Academy of Sciences of the United States of America. 1996, 93: 13-20. 10.1073\/pnas.93.1.13.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"6369_CR4","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000, 28: 235-242. 10.1093\/nar\/28.1.235.","journal-title":"Nucleic Acids Res"},{"key":"6369_CR5","doi-asserted-by":"publisher","first-page":"704","DOI":"10.1002\/prot.21804","volume":"69","author":"MF Lensink","year":"2007","unstructured":"Lensink MF, Mendez R, Wodak SJ: Docking and scoring protein complexes: CAPRI 3rd Edition. Proteins. 2007, 69: 704-718. 10.1002\/prot.21804.","journal-title":"Proteins"},{"key":"6369_CR6","doi-asserted-by":"publisher","first-page":"150","DOI":"10.1002\/prot.20551","volume":"60","author":"R Mendez","year":"2005","unstructured":"Mendez R, Leplae R, Lensink MF, Wodak SJ: Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins. 2005, 60: 150-169. 10.1002\/prot.20551.","journal-title":"Proteins"},{"key":"6369_CR7","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1038\/nsb0902-646","volume":"9","author":"M Karplus","year":"2002","unstructured":"Karplus M, McCammon JA: Molecular dynamics simulations of biomolecules. Nature structural biology. 2002, 9: 646-652. 10.1038\/nsb0902-646.","journal-title":"Nature structural biology"},{"key":"6369_CR8","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1146\/annurev.biophys.30.1.211","volume":"30","author":"W Wang","year":"2001","unstructured":"Wang W, Donini O, Reyes CM, Kollman PA: Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein- ligand, protein-protein, and protein-nucleic acid noncovalent interactions. Annual review of biophysics and biomolecular structure. 2001, 30: 211-243. 10.1146\/annurev.biophys.30.1.211.","journal-title":"Annual review of biophysics and biomolecular structure"},{"key":"6369_CR9","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1016\/S0959-440X(02)00308-1","volume":"12","author":"T Hansson","year":"2002","unstructured":"Hansson T, Oostenbrink C, van Gunsteren W: Molecular dynamics simulations. Current opinion in structural biology. 2002, 12: 190-196. 10.1016\/S0959-440X(02)00308-1.","journal-title":"Current opinion in structural biology"},{"key":"6369_CR10","doi-asserted-by":"publisher","first-page":"6679","DOI":"10.1073\/pnas.0408930102","volume":"102","author":"M Karplus","year":"2005","unstructured":"Karplus M, Kuriyan J: Molecular dynamics and protein function. Proceedings of the National Academy of Sciences of the United States of America. 2005, 102: 6679-6685. 10.1073\/pnas.0408930102.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"6369_CR11","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1021\/ct700301q","volume":"4","author":"B Hess","year":"2008","unstructured":"Hess B, Kutzner C, van der Spoel D, Lindahl E: GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of chemical theory and computation. 2008, 4: 435-447. 10.1021\/ct700301q.","journal-title":"Journal of chemical theory and computation"},{"key":"6369_CR12","doi-asserted-by":"publisher","first-page":"1542","DOI":"10.1021\/ct200909j","volume":"8","author":"AW Gotz","year":"2012","unstructured":"Gotz AW, Williamson MJ, Xu D, Poole D, Le Grand S, Walker RC: Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born. Journal of chemical theory and computation. 2012, 8: 1542-1555. 10.1021\/ct200909j.","journal-title":"Journal of chemical theory and computation"},{"key":"6369_CR13","doi-asserted-by":"publisher","first-page":"845","DOI":"10.1093\/bioinformatics\/btt055","volume":"29","author":"S Pronk","year":"2013","unstructured":"Pronk S, Pall S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, Shirts MR, Smith JC, Kasson PM, van der Spoel D: GROMACS 4.5: a high- throughput and highly parallel open source molecular simulation toolkit. Bioinformatics. 2013, 29: 845-854. 10.1093\/bioinformatics\/btt055.","journal-title":"Bioinformatics"},{"key":"6369_CR14","doi-asserted-by":"publisher","first-page":"3276","DOI":"10.1093\/bioinformatics\/btr550","volume":"27","author":"P Schmidtke","year":"2011","unstructured":"Schmidtke P, Bidon-Chanal A, Luque FJ, Barril X: MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories. Bioinformatics. 2011, 27: 3276-3285. 10.1093\/bioinformatics\/btr550.","journal-title":"Bioinformatics"},{"key":"6369_CR15","doi-asserted-by":"publisher","first-page":"773","DOI":"10.1016\/j.jmgm.2010.10.007","volume":"29","author":"JD Durrant","year":"2011","unstructured":"Durrant JD, de Oliveira CA, McCammon JA: POVME: an algorithm for measuring binding-pocket volumes. Journal of molecular graphics & modelling. 2011, 29: 773-776. 10.1016\/j.jmgm.2010.10.007.","journal-title":"Journal of molecular graphics & modelling"},{"key":"6369_CR16","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1016\/j.jmgm.2011.07.008","volume":"31","author":"JD Durrant","year":"2011","unstructured":"Durrant JD, McCammon JA: HBonanza: a computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis. Journal of molecular graphics & modelling. 2011, 31: 5-9.","journal-title":"Journal of molecular graphics & modelling"},{"key":"6369_CR17","doi-asserted-by":"publisher","first-page":"1007","DOI":"10.1093\/bioinformatics\/btl059","volume":"22","author":"SB Dixit","year":"2006","unstructured":"Dixit SB, Beveridge DL: Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction. Bioinformatics. 2006, 22: 1007-1009. 10.1093\/bioinformatics\/btl059.","journal-title":"Bioinformatics"},{"key":"6369_CR18","doi-asserted-by":"publisher","first-page":"2915","DOI":"10.1093\/bioinformatics\/btr484","volume":"27","author":"A Vangone","year":"2011","unstructured":"Vangone A, Spinelli R, Scarano V, Cavallo L, Oliva R: COCOMAPS: a web application to analyze and visualize contacts at the interface of biomolecular complexes. Bioinformatics. 2011, 27: 2915-2916. 10.1093\/bioinformatics\/btr484.","journal-title":"Bioinformatics"},{"issue":"Suppl 4","key":"6369_CR19","doi-asserted-by":"publisher","first-page":"S19","DOI":"10.1186\/1471-2105-13-S4-S19","volume":"13","author":"A Vangone","year":"2012","unstructured":"Vangone A, Oliva R, Cavallo L: CONS-COCOMAPS: a novel tool to measure and visualize the conservation of inter-residue contacts in multiple docking solutions. Bmc Bioinformatics. 2012, 13 (Suppl 4): S19-10.1186\/1471-2105-13-S4-S19.","journal-title":"Bmc Bioinformatics"},{"key":"6369_CR20","doi-asserted-by":"publisher","first-page":"1571","DOI":"10.1002\/prot.24314","volume":"81","author":"R Oliva","year":"2013","unstructured":"Oliva R, Vangone A, Cavallo L: Ranking multiple docking solutions based on the conservation of inter-residue contacts. Proteins. 2013, 81: 1571-1584. 10.1002\/prot.24314.","journal-title":"Proteins"},{"key":"6369_CR21","doi-asserted-by":"publisher","first-page":"2210","DOI":"10.1002\/prot.24423","volume":"81","author":"A Vangone","year":"2013","unstructured":"Vangone A, Cavallo L, Oliva R: Using a consensus approach based on the conservation of inter-residue contacts to rank CAPRI models. Proteins. 2013, 81: 2210-2220. 10.1002\/prot.24423.","journal-title":"Proteins"},{"key":"6369_CR22","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1002\/prot.10393","volume":"52","author":"R Mendez","year":"2003","unstructured":"Mendez R, Leplae R, De Maria L, Wodak SJ: Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins. 2003, 52: 51-67. 10.1002\/prot.10393.","journal-title":"Proteins"},{"key":"6369_CR23","doi-asserted-by":"crossref","first-page":"1810","DOI":"10.1002\/prot.24078","volume":"80","author":"JP Rodrigues","year":"2012","unstructured":"Rodrigues JP, Trellet M, Schmitz C, Kastritis P, Karaca E, Melquiond AS, Bonvin AM: Clustering biomolecular complexes by residue contacts similarity. Proteins. 2012, 80: 1810-1817.","journal-title":"Proteins"},{"key":"6369_CR24","doi-asserted-by":"publisher","first-page":"2216","DOI":"10.1021\/pr9009854","volume":"9","author":"PL Kastritis","year":"2010","unstructured":"Kastritis PL, Bonvin AMJJ: Are Scoring Functions in Protein-Protein Docking Ready To Predict Interactomes? Clues from a Novel Binding Affinity Benchmark. Journal of Proteome Research. 2010, 9: 2216-2225. 10.1021\/pr9009854.","journal-title":"Journal of Proteome Research"},{"key":"6369_CR25","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1016\/S0969-2126(99)80012-4","volume":"7","author":"TP Ko","year":"1999","unstructured":"Ko TP, Liao CC, Ku WY, Chak KF, Yuan HS: The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor Im7 protein. Structure with Folding & Design. 1999, 7: 91-102.","journal-title":"Structure with Folding & Design"},{"key":"6369_CR26","doi-asserted-by":"publisher","first-page":"791","DOI":"10.1016\/S0092-8674(00)80790-4","volume":"97","author":"JH Wang","year":"1999","unstructured":"Wang JH, Smolyar A, Tan K, Liu JH, Kim M, Sun ZY, Wagner G, Reinherz EL: Structure of a heterophilic adhesion complex between the human CD2 and CD58 (LFA-3) counterreceptors. Cell. 1999, 97: 791-803. 10.1016\/S0092-8674(00)80790-4.","journal-title":"Cell"},{"key":"6369_CR27","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.4315\/0362-028X-65.9.1381","volume":"65","author":"GP Schamberger","year":"2002","unstructured":"Schamberger GP, Diez-Gonzalez F: Selection of recently isolated colicinogenic Escherichia coli strains inhibitory to Escherichia coli O157:H7. Journal of food protection. 2002, 65: 1381-1387.","journal-title":"Journal of food protection"},{"key":"6369_CR28","doi-asserted-by":"crossref","first-page":"847","DOI":"10.4315\/0362-028X-66.5.847","volume":"66","author":"SE Murinda","year":"2003","unstructured":"Murinda SE, Rashid KA, Roberts RF: In vitro assessment of the cytotoxicity of nisin, pediocin, and selected colicins on simian virus 40-transfected human colon and Vero monkey kidney cells with trypan blue staining viability assays. Journal of food protection. 2003, 66: 847-853.","journal-title":"Journal of food protection"},{"key":"6369_CR29","doi-asserted-by":"publisher","first-page":"371","DOI":"10.1038\/nsmb749","volume":"11","author":"T Kortemme","year":"2004","unstructured":"Kortemme T, Joachimiak LA, Bullock AN, Schuler AD, Stoddard BL, Baker D: Computational redesign of protein-protein interaction specificity. Nature structural & molecular biology. 2004, 11: 371-379. 10.1038\/nsmb749.","journal-title":"Nature structural & molecular biology"},{"key":"6369_CR30","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/j.jmb.2006.05.022","volume":"361","author":"LA Joachimiak","year":"2006","unstructured":"Joachimiak LA, Kortemme T, Stoddard BL, Baker D: Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface. Journal of molecular biology. 2006, 361: 195-208. 10.1016\/j.jmb.2006.05.022.","journal-title":"Journal of molecular biology"},{"key":"6369_CR31","doi-asserted-by":"publisher","first-page":"1303","DOI":"10.1021\/cr9603744","volume":"97","author":"JC Ma","year":"1997","unstructured":"Ma JC, Dougherty DA: The Cationminus signpi Interaction. Chem Rev. 1997, 97: 1303-1324. 10.1021\/cr9603744.","journal-title":"Chem Rev"},{"key":"6369_CR32","doi-asserted-by":"publisher","first-page":"4462","DOI":"10.4049\/jimmunol.168.9.4462","volume":"168","author":"AJ da Silva","year":"2002","unstructured":"da Silva AJ, Brickelmaier M, Majeau GR, Li Z, Su L, Hsu YM, Hochman PS: Alefacept, an immunomodulatory recombinant LFA-3\/IgG1 fusion protein, induces CD16 signaling and CD2\/CD16-dependent apoptosis of CD2(+) cells. J Immunol. 2002, 168: 4462-4471. 10.4049\/jimmunol.168.9.4462.","journal-title":"J Immunol"},{"key":"6369_CR33","doi-asserted-by":"publisher","first-page":"591","DOI":"10.1046\/j.1365-2230.2002.01171.x","volume":"27","author":"U Mrowietz","year":"2002","unstructured":"Mrowietz U: Treatment targeted to cell surface epitopes. Clinical and experimental dermatology. 2002, 27: 591-596. 10.1046\/j.1365-2230.2002.01171.x.","journal-title":"Clinical and experimental dermatology"},{"key":"6369_CR34","doi-asserted-by":"publisher","first-page":"1748","DOI":"10.1097\/01.TP.0000064211.23536.AD","volume":"75","author":"TR Spitzer","year":"2003","unstructured":"Spitzer TR, McAfee SL, Dey BR, Colby C, Hope J, Grossberg H, Preffer F, Shaffer J, Alexander SI, Sachs DH: Nonmyeloablative haploidentical stem-cell transplantation using anti-CD2 monoclonal antibody (MEDI-507)- based conditioning for refractory hematologic malignancies. Transplantation. 2003, 75: 1748-1751. 10.1097\/01.TP.0000064211.23536.AD.","journal-title":"Transplantation"},{"key":"6369_CR35","doi-asserted-by":"publisher","first-page":"187","DOI":"10.2165\/00063030-200317030-00005","volume":"17","author":"J Braun","year":"2003","unstructured":"Braun J, Sieper J: Role of novel biological therapies in psoriatic arthritis: effects on joints and skin. BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy. 2003, 17: 187-199. 10.2165\/00063030-200317030-00005.","journal-title":"BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy"},{"key":"6369_CR36","doi-asserted-by":"publisher","first-page":"810","DOI":"10.1111\/j.1476-5381.2010.00702.x","volume":"160","author":"W Weger","year":"2010","unstructured":"Weger W: Current status and new developments in the treatment of psoriasis and psoriatic arthritis with biological agents. British journal of pharmacology. 2010, 160: 810-820. 10.1111\/j.1476-5381.2010.00702.x.","journal-title":"British journal of pharmacology"},{"key":"6369_CR37","doi-asserted-by":"publisher","first-page":"5307","DOI":"10.1021\/jm200004e","volume":"54","author":"A Gokhale","year":"2011","unstructured":"Gokhale A, Weldeghiorghis TK, Taneja V, Satyanarayanajois SD: Conformationally constrained peptides from CD2 to modulate protein- protein interactions between CD2 and CD58. Journal of medicinal chemistry. 2011, 54: 5307-5319. 10.1021\/jm200004e.","journal-title":"Journal of medicinal chemistry"},{"key":"6369_CR38","doi-asserted-by":"publisher","first-page":"1439","DOI":"10.1084\/jem.177.5.1439","volume":"177","author":"AR Arulanandam","year":"1993","unstructured":"Arulanandam AR, Moingeon P, Concino MF, Recny MA, Kato K, Yagita H, Koyasu S, Reinherz EL: A soluble multimeric recombinant CD2 protein identifies CD48 as a low affinity ligand for human CD2: divergence of CD2 ligands during the evolution of humans and mice. J Exp Med. 1993, 177: 1439-1450. 10.1084\/jem.177.5.1439.","journal-title":"J Exp Med"},{"key":"6369_CR39","doi-asserted-by":"publisher","first-page":"15782","DOI":"10.1074\/jbc.272.25.15782","volume":"272","author":"ML Dustin","year":"1997","unstructured":"Dustin ML: Adhesive bond dynamics in contacts between T lymphocytes and glass-supported planar bilayers reconstituted with the immunoglobulin- related adhesion molecule CD58. The Journal of biological chemistry. 1997, 272: 15782-15788. 10.1074\/jbc.272.25.15782.","journal-title":"The Journal of biological chemistry"},{"key":"6369_CR40","doi-asserted-by":"crossref","first-page":"8542","DOI":"10.1016\/S0021-9258(19)38922-7","volume":"265","author":"MA Recny","year":"1990","unstructured":"Recny MA, Neidhardt EA, Sayre PH, Ciardelli TL, Reinherz EL: Structural and functional characterization of the CD2 immunoadhesion domain. Evidence for inclusion of CD2 in an alpha-beta protein folding class. The Journal of biological chemistry. 1990, 265: 8542-8549.","journal-title":"The Journal of biological chemistry"},{"key":"6369_CR41","doi-asserted-by":"publisher","first-page":"995","DOI":"10.1084\/jem.169.3.995","volume":"169","author":"PH Sayre","year":"1989","unstructured":"Sayre PH, Hussey RE, Chang HC, Ciardelli TL, Reinherz EL: Structural and binding analysis of a two domain extracellular CD2 molecule. J Exp Med. 1989, 169: 995-1009. 10.1084\/jem.169.3.995.","journal-title":"J Exp Med"},{"key":"6369_CR42","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1074\/jbc.270.1.369","volume":"270","author":"SJ Davis","year":"1995","unstructured":"Davis SJ, Davies EA, Barclay AN, Daenke S, Bodian DL, Jones EY, Stuart DI, Butters TD, Dwek RA, van der Merwe PA: Ligand binding by the immunoglobulin superfamily recognition molecule CD2 is glycosylation- independent. The Journal of biological chemistry. 1995, 270: 369-375. 10.1074\/jbc.270.1.369.","journal-title":"The Journal of biological chemistry"},{"key":"6369_CR43","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1111\/j.1600-065X.1998.tb01199.x","volume":"163","author":"SJ Davis","year":"1998","unstructured":"Davis SJ, Ikemizu S, Wild MK, van der Merwe PA: CD2 and the nature of protein interactions mediating cell-cell recognition. Immunol Rev. 1998, 163: 217-236. 10.1111\/j.1600-065X.1998.tb01199.x.","journal-title":"Immunol Rev"},{"key":"6369_CR44","doi-asserted-by":"crossref","first-page":"1950","DOI":"10.1002\/prot.22711","volume":"78","author":"K Lindorff-Larsen","year":"2010","unstructured":"Lindorff-Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, Dror RO, Shaw DE: Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins. 2010, 78: 1950-1958.","journal-title":"Proteins"},{"key":"6369_CR45","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. Journal of Chemical Physics. 1983, 79: 926-935. 10.1063\/1.445869.","journal-title":"Journal of Chemical Physics"},{"key":"6369_CR46","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1098\/rsta.1993.0120","volume":"345","author":"WL Jorgensen","year":"1993","unstructured":"Jorgensen WL, Duffy EM, Tiradorives J: Computational Investigations of Protein Denaturation - Apomyoglobin and Chaotrope-Arene Interactions. Philos T R Soc A. 1993, 345: 87-96. 10.1098\/rsta.1993.0120.","journal-title":"Philos T R Soc A"},{"key":"6369_CR47","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.Log(N) Method for Ewald Sums in Large Systems. Journal of Chemical Physics. 1993, 98: 10089-10092. 10.1063\/1.464397.","journal-title":"Journal of Chemical Physics"},{"key":"6369_CR48","doi-asserted-by":"publisher","first-page":"1463","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H","volume":"18","author":"B Hess","year":"1997","unstructured":"Hess B, Bekker H, Berendsen HJC, Fraaije JGEM: LINCS: A linear constraint solver for molecular simulations. Journal of computational chemistry. 1997, 18: 1463-1472. 10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H.","journal-title":"Journal of computational chemistry"},{"key":"6369_CR49","doi-asserted-by":"publisher","first-page":"014101","DOI":"10.1063\/1.2408420","volume":"126","author":"G Bussi","year":"2007","unstructured":"Bussi G, Donadio D, Parrinello M: Canonical sampling through velocity rescaling. The Journal of chemical physics. 2007, 126: 014101-10.1063\/1.2408420.","journal-title":"The Journal of chemical physics"},{"key":"6369_CR50","doi-asserted-by":"publisher","first-page":"7182","DOI":"10.1063\/1.328693","volume":"52","author":"M Parrinello","year":"1981","unstructured":"Parrinello M, Rahman A: Polymorphic Transitions in Single-Crystals - a New Molecular-Dynamics Method. J Appl Phys. 1981, 52: 7182-7190. 10.1063\/1.328693.","journal-title":"J Appl Phys"},{"key":"6369_CR51","doi-asserted-by":"publisher","first-page":"1707","DOI":"10.1016\/S0006-3495(96)79372-4","volume":"71","author":"BL de Groot","year":"1996","unstructured":"de Groot BL, van Aalten DM, Amadei A, Berendsen HJ: The consistency of large concerted motions in proteins in molecular dynamics simulations. Biophysical journal. 1996, 71: 1707-1713. 10.1016\/S0006-3495(96)79372-4.","journal-title":"Biophysical journal"},{"key":"6369_CR52","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1002\/(SICI)1097-0134(19990901)36:4<419::AID-PROT5>3.0.CO;2-U","volume":"36","author":"A Amadei","year":"1999","unstructured":"Amadei A, Ceruso MA, Di Nola A: On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations. Proteins. 1999, 36: 419-424. 10.1002\/(SICI)1097-0134(19990901)36:4<419::AID-PROT5>3.0.CO;2-U.","journal-title":"Proteins"},{"key":"6369_CR53","volume-title":"'NACCESS' Computer Program. Department of Biochemistry and Molecular Biology","author":"SJ Hubbard","year":"1993","unstructured":"Hubbard SJ, Thornton JM: 'NACCESS' Computer Program. Department of Biochemistry and Molecular Biology. 1993, University College London"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-15-S5-S1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,26]],"date-time":"2024-05-26T12:38:34Z","timestamp":1716727114000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-15-S5-S1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,5]]},"references-count":53,"journal-issue":{"issue":"S5","published-print":{"date-parts":[[2014,5]]}},"alternative-id":["6369"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-15-s5-s1","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,5]]},"assertion":[{"value":"6 May 2014","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S1"}}