{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,22]],"date-time":"2025-11-22T11:07:17Z","timestamp":1763809637754,"version":"3.37.3"},"reference-count":56,"publisher":"Springer Science and Business Media LLC","issue":"2","license":[{"start":{"date-parts":[[2017,1,19]],"date-time":"2017-01-19T00:00:00Z","timestamp":1484784000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"funder":[{"name":"Department of Biotechnology, Government of India"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Comput Aided Mol Des"],"published-print":{"date-parts":[[2017,2]]},"DOI":"10.1007\/s10822-016-0007-0","type":"journal-article","created":{"date-parts":[[2017,1,19]],"date-time":"2017-01-19T12:50:21Z","timestamp":1484830221000},"page":"219-235","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["RNAHelix: computational modeling of nucleic acid structures with Watson\u2013Crick and non-canonical base pairs"],"prefix":"10.1007","volume":"31","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9227-6490","authenticated-orcid":false,"given":"Dhananjay","family":"Bhattacharyya","sequence":"first","affiliation":[]},{"given":"Sukanya","family":"Halder","sequence":"additional","affiliation":[]},{"given":"Sankar","family":"Basu","sequence":"additional","affiliation":[]},{"given":"Debasish","family":"Mukherjee","sequence":"additional","affiliation":[]},{"given":"Prasun","family":"Kumar","sequence":"additional","affiliation":[]},{"given":"Manju","family":"Bansal","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2017,1,19]]},"reference":[{"key":"7_CR1","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1126\/science.185.4149.435","volume":"185","author":"SH Kim","year":"1974","unstructured":"Kim SH, Suddath FL, Quigley GJ et al (1974) Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science 185:435\u2013440. doi: 10.1126\/science.185.4149.435","journal-title":"Science"},{"key":"7_CR2","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1038\/353579a0","volume":"353","author":"SR Holbrook","year":"1991","unstructured":"Holbrook SR, Cheong C, Tinoco I, Kim SH (1991) Crystal structure of an RNA double helix incorporating a track of non-Watson\u2013Crick base pairs. Nature 353:579\u2013581","journal-title":"Nature"},{"key":"7_CR3","doi-asserted-by":"crossref","first-page":"4160","DOI":"10.1073\/pnas.91.10.4160","volume":"91","author":"WB Cruse","year":"1994","unstructured":"Cruse WB, Saludjian P, Biala E et al (1994) Structure of a mispaired RNA double helix at 1.6-A resolution and implications for the prediction of RNA secondary structure. Proc Natl Acad Sci USA 91:4160\u20134164","journal-title":"Proc Natl Acad Sci USA"},{"key":"7_CR4","doi-asserted-by":"publisher","first-page":"8489","DOI":"10.1021\/bi9607214","volume":"35","author":"M Egli","year":"1996","unstructured":"Egli M, Portmann S, Usman N (1996) RNA hydration: a detailed look \u2020, \u2021. BioChemistry 35:8489\u20138494. doi: 10.1021\/bi9607214","journal-title":"BioChemistry"},{"key":"7_CR5","doi-asserted-by":"publisher","first-page":"6240","DOI":"10.1021\/ja069366n","volume":"129","author":"T Lenz","year":"2007","unstructured":"Lenz T, Bonnist EYM, Pljevalj\u010di\u0107 G et al (2007) 2-aminopurine flipped into the active site of the adenine-specific DNA methyltransferase M. TaqI: crystal structures and time-resolved fluorescence. J Am Chem Soc 129:6240\u20136248. doi: 10.1021\/ja069366n","journal-title":"J Am Chem Soc"},{"key":"7_CR6","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1017\/S1355838201002515","volume":"7","author":"NB Leontis","year":"2001","unstructured":"Leontis NB, Westhof E (2001) Geometric nomenclature and classification of RNA base pairs. RNA 7:499\u2013512","journal-title":"RNA"},{"key":"7_CR7","doi-asserted-by":"publisher","unstructured":"Bhattacharya S, Mittal S, Panigrahi S, et al. (2015) RNABP COGEST: a resource for investigating functional RNAs. Database (Oxford) bav011. doi: 10.1093\/database\/bav011","DOI":"10.1093\/database\/bav011"},{"key":"7_CR8","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1006\/jmbi.2001.4987","volume":"313","author":"WK Olson","year":"2001","unstructured":"Olson WK, Bansal M, Burley SK et al (2001) A standard reference frame for the description of nucleic acid base-pair geometry. J Mol Biol 313:229\u2013237. doi: 10.1006\/jmbi.2001.4987","journal-title":"J Mol Biol"},{"key":"7_CR9","doi-asserted-by":"publisher","first-page":"627","DOI":"10.1080\/07391102.1989.10507726","volume":"6","author":"RE Dickerson","year":"1989","unstructured":"Dickerson RE (1989) Definitions and nomenclature of nucleic acid structure parameters. J Biomol Struct Dyn 6:627\u2013634. doi: 10.1080\/07391102.1989.10507726","journal-title":"J Biomol Struct Dyn"},{"key":"7_CR10","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1016\/0022-2836(82)90157-7","volume":"161","author":"CR Calladine","year":"1982","unstructured":"Calladine CR (1982) Mechanics of sequence-dependent stacking of bases in B-DNA. J Mol Biol 161:343\u2013352. doi: 10.1016\/0022-2836(82)90157-7","journal-title":"J Mol Biol"},{"key":"7_CR11","doi-asserted-by":"publisher","first-page":"669","DOI":"10.1080\/07391102.1989.10507729","volume":"6","author":"G Ravishanker","year":"1989","unstructured":"Ravishanker G, Swaminathan S, Beveridge DL et al (1989) Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: \u201ccurves\u201d, dials and windows. J Biomol Struct Dyn 6:669\u2013699. doi: 10.1080\/07391102.1989.10507729","journal-title":"J Biomol Struct Dyn"},{"key":"7_CR12","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1080\/07391102.1990.10507828","volume":"8","author":"D Bhattacharyya","year":"1990","unstructured":"Bhattacharyya D, Bansal M (1990) Local variability and base sequence effects in DNA crystal structures. J Biomol Struct Dyn 8:539\u2013572. doi: 10.1080\/07391102.1990.10507828","journal-title":"J Biomol Struct Dyn"},{"key":"7_CR13","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1006\/jmbi.1994.1212","volume":"237","author":"MS Babcock","year":"1994","unstructured":"Babcock MS, Olson WK (1994) The effect of mathematics and coordinate system on comparability and \u201cdependencies\u201d of nucleic acid structure parameters. J Mol Biol 237:98\u2013124. doi: 10.1006\/jmbi.1994.1212","journal-title":"J Mol Biol"},{"key":"7_CR14","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1080\/07391102.2000.10506645","volume":"18","author":"D Bandyopadhyay","year":"2000","unstructured":"Bandyopadhyay D, Bhattacharyya D (2000) Effect of neighboring bases on base-pair stacking orientation: a molecular dynamics study. J Biomol Struct Dyn 18:29\u201343. doi: 10.1080\/07391102.2000.10506645","journal-title":"J Biomol Struct Dyn"},{"key":"7_CR15","doi-asserted-by":"publisher","first-page":"3799","DOI":"10.1529\/biophysj.104.045252","volume":"87","author":"DL Beveridge","year":"2004","unstructured":"Beveridge DL, Barreiro G, Suzie Byun K et al (2004) Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps. Biophys J 87:3799\u20133813. doi: 10.1529\/biophysj.104.045252","journal-title":"Biophys J"},{"key":"7_CR16","doi-asserted-by":"publisher","first-page":"6063","DOI":"10.1093\/nar\/gkm627","volume":"35","author":"S Fujii","year":"2007","unstructured":"Fujii S, Kono H, Takenaka S et al (2007) Sequence-dependent DNA deformability studied using molecular dynamics simulations. Nucleic Acids Res 35:6063\u20136074. doi: 10.1093\/nar\/gkm627","journal-title":"Nucleic Acids Res"},{"key":"7_CR17","doi-asserted-by":"publisher","first-page":"1097","DOI":"10.1016\/S0022-2836(02)00386-8","volume":"319","author":"CA Davey","year":"2002","unstructured":"Davey CA, Sargent DF, Luger K et al (2002) Solvent mediated interactions in the structure of the nucleosome core particle at 1.9\u00a0\u00c5 resolution. J Mol Biol 319:1097\u20131113. doi: 10.1016\/S0022-2836(02)00386-8","journal-title":"J Mol Biol"},{"key":"7_CR18","doi-asserted-by":"publisher","first-page":"528","DOI":"10.1016\/j.str.2010.01.015","volume":"18","author":"B Wu","year":"2010","unstructured":"Wu B, Mohideen K, Vasudevan D, Davey CA (2010) Structural insight into the sequence dependence of nucleosome positioning. Structure 18:528\u2013536. doi: 10.1016\/j.str.2010.01.015","journal-title":"Structure"},{"key":"7_CR19","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1146\/annurev-biophys-042910-155329","volume":"40","author":"AJ Andrews","year":"2011","unstructured":"Andrews AJ, Luger K (2011) Nucleosome structure(s) and stability: variations on a theme. Annu Rev Biophys 40:99\u2013117. doi: 10.1146\/annurev-biophys-042910-155329","journal-title":"Annu Rev Biophys"},{"key":"7_CR20","doi-asserted-by":"publisher","first-page":"14028","DOI":"10.1021\/jp102835t","volume":"114","author":"S Halder","year":"2010","unstructured":"Halder S, Bhattacharyya D (2010) Structural stability of tandemly occurring noncanonical basepairs within double helical fragments: molecular dynamics studies of functional RNA. J Phys Chem B 114:14028\u201314040. doi: 10.1021\/jp102835t","journal-title":"J Phys Chem B"},{"key":"7_CR21","doi-asserted-by":"publisher","first-page":"11845","DOI":"10.1021\/jp305628v","volume":"116","author":"S Halder","year":"2012","unstructured":"Halder S, Bhattacharyya D (2012) Structural variations of single and tandem mismatches in RNA duplexes: a joint MD simulation and crystal structure database analysis. J Phys Chem B 116:11845\u201311856. doi: 10.1021\/jp305628v","journal-title":"J Phys Chem B"},{"key":"7_CR22","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 et al (2000) The protein data bank. Nucleic Acids Res 28:235\u2013242. doi: 10.1093\/nar\/28.1.235","journal-title":"Nucleic Acids Res"},{"key":"7_CR23","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1080\/07391102.1991.10507898","volume":"9","author":"D Mohanty","year":"1991","unstructured":"Mohanty D, Bansal M (1991) DNA polymorphism and local variation in base-pair orientation: a theoretical rationale. J Biomol Struct Dyn 9:127\u2013142. doi: 10.1080\/07391102.1991.10507898","journal-title":"J Biomol Struct Dyn"},{"key":"7_CR24","doi-asserted-by":"publisher","first-page":"1025","DOI":"10.1006\/jmbi.1993.1217","volume":"230","author":"CA Hunter","year":"1993","unstructured":"Hunter CA (1993) Sequence-dependent DNA structure. The role of base stacking interactions. J Mol Biol 230:1025\u20131054. doi: 10.1006\/jmbi.1993.1217","journal-title":"J Mol Biol"},{"key":"7_CR25","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1002\/bip.22787","volume":"105","author":"M Mondal","year":"2016","unstructured":"Mondal M, Halder S, Chakrabarti J, Bhattacharyya D (2016) Hybrid simulation approach incorporating microscopic interaction along with rigid body degrees of freedom for stacking between base pairs. Biopolymers 105:212\u2013226. doi: 10.1002\/bip.22787","journal-title":"Biopolymers"},{"key":"7_CR26","doi-asserted-by":"publisher","first-page":"5108","DOI":"10.1093\/nar\/gkg680","volume":"31","author":"X-JXJ Lu","year":"2003","unstructured":"Lu X-JXJ, Olson WK (2003) 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res 31:5108\u20135121. doi: 10.1093\/nar\/gkg680","journal-title":"Nucleic Acids Res"},{"key":"7_CR27","doi-asserted-by":"publisher","first-page":"1213","DOI":"10.1038\/nprot.2008.104","volume":"3","author":"X-J Lu","year":"2008","unstructured":"Lu X-J, Olson WK (2008) 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nat Protoc 3:1213\u20131227. doi: 10.1038\/nprot.2008.104","journal-title":"Nat Protoc"},{"key":"7_CR28","doi-asserted-by":"publisher","first-page":"W235","DOI":"10.1093\/nar\/gkp287","volume":"37","author":"M Dijk van","year":"2009","unstructured":"van Dijk M, Bonvin AMJJ (2009) 3D-DART: a DNA structure modelling server. Nucleic Acids Res 37:W235\u2013W239. doi: 10.1093\/nar\/gkp287","journal-title":"Nucleic Acids Res"},{"key":"7_CR29","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1093\/bioinformatics\/11.3.281","volume":"11","author":"M Bansal","year":"1995","unstructured":"Bansal M, Bhattacharyya D, Ravi B (1995) NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures. Bioinformatics 11:281\u2013287. doi: 10.1093\/bioinformatics\/11.3.281","journal-title":"Bioinformatics"},{"key":"7_CR30","doi-asserted-by":"crossref","unstructured":"Macke TJ, Case DA (1997) Modeling unusual nucleic acid structures. In: ACS Symp. Ser. pp\u00a0379\u2013393","DOI":"10.1021\/bk-1998-0682.ch024"},{"key":"7_CR31","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1038\/nature06684","volume":"452","author":"M Parisien","year":"2008","unstructured":"Parisien M, Major F (2008) The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature 452:51\u201355. doi: 10.1038\/nature06684","journal-title":"Nature"},{"key":"7_CR32","doi-asserted-by":"publisher","first-page":"e112","DOI":"10.1093\/nar\/gks339","volume":"40","author":"M Popenda","year":"2012","unstructured":"Popenda M, Szachniuk M, Antczak M et al (2012) Automated 3D structure composition for large RNAs. Nucleic Acids Res 40:e112. doi: 10.1093\/nar\/gks339","journal-title":"Nucleic Acids Res"},{"key":"7_CR33","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1006\/jmbi.1997.1345","volume":"273","author":"X-J Lu","year":"1997","unstructured":"Lu X-J, El Hassan MA, Hunter CA (1997) Structure and conformation of helical nucleic acids: rebuilding program (SCHNArP). J Mol Biol 273:681\u2013691. doi: 10.1006\/jmbi.1997.1345","journal-title":"J Mol Biol"},{"key":"7_CR34","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1080\/07391102.1988.10506484","volume":"6","author":"D Bhattacharya","year":"1988","unstructured":"Bhattacharya D, Bansal M (1988) A general procedure for generation of curved DNA molecules. J Biomol Struct Dyn 6:93\u2013104. doi: 10.1080\/07391102.1988.10506484","journal-title":"J Biomol Struct Dyn"},{"key":"7_CR35","doi-asserted-by":"publisher","first-page":"635","DOI":"10.1080\/07391102.1989.10507727","volume":"6","author":"D Bhattacharyya","year":"1989","unstructured":"Bhattacharyya D, Bansal M (1989) A self-consistent formulation for analysis and generation of non-uniform DNA structures. J Biomol Struct Dyn 6:635\u2013653. doi: 10.1080\/07391102.1989.10507727","journal-title":"J Biomol Struct Dyn"},{"key":"7_CR36","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1007\/s10822-006-9083-x","volume":"20","author":"S Mukherjee","year":"2006","unstructured":"Mukherjee S, Bansal M, Bhattacharyya D (2006) Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis. J Comput Aided Mol Des 20:629\u2013645. doi: 10.1007\/s10822-006-9083-x","journal-title":"J Comput Aided Mol Des"},{"key":"7_CR37","doi-asserted-by":"publisher","first-page":"1545","DOI":"10.1002\/jcc.21287","volume":"30","author":"BR Brooks","year":"2009","unstructured":"Brooks BR, Brooks CL, Mackerell AD et al (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30:1545\u20131614. doi: 10.1002\/jcc.21287","journal-title":"J Comput Chem"},{"key":"7_CR38","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1080\/07391102.2006.10507108","volume":"24","author":"J Das","year":"2006","unstructured":"Das J, Mukherjee S, Mitra A, Bhattacharyya D (2006) Non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis. J Biomol Struct Dyn 24:149\u2013161. doi: 10.1080\/07391102.2006.10507108","journal-title":"J Biomol Struct Dyn"},{"key":"7_CR39","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1080\/07391102.2011.10507404","volume":"29","author":"S Panigrahi","year":"2011","unstructured":"Panigrahi S, Pal R, Bhattacharyya D (2011) Structure and energy of non-canonical basepairs: comparison of various computational chemistry methods with crystallographic ensembles. J Biomol Struct Dyn 29:541\u2013556. doi: 10.1080\/07391102.2011.10507404","journal-title":"J Biomol Struct Dyn"},{"key":"7_CR40","doi-asserted-by":"publisher","first-page":"59","DOI":"10.3389\/fgene.2012.00059","volume":"3","author":"SS Ray","year":"2012","unstructured":"Ray SS, Halder S, Kaypee S, Bhattacharyya D (2012) HD-RNAS: an automated hierarchical database of RNA structures. Front Genet 3:59. doi: 10.3389\/fgene.2012.00059","journal-title":"Front Genet"},{"key":"7_CR41","doi-asserted-by":"publisher","first-page":"1327","DOI":"10.1261\/rna.039438.113","volume":"19","author":"AI Petrov","year":"2013","unstructured":"Petrov AI, Zirbel CL, Leontis NB (2013) Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas. RNA 19:1327\u20131340. doi: 10.1261\/rna.039438.113","journal-title":"RNA"},{"key":"7_CR42","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1021\/ja952883d","volume":"118","author":"L Clowney","year":"1996","unstructured":"Clowney L, Jain SC, Srinivasan AR et al (1996) Geometric parameters in nucleic acids: nitrogenous bases. J Am Chem Soc 118:509\u2013518. doi: 10.1021\/ja952883d","journal-title":"J Am Chem Soc"},{"key":"7_CR43","doi-asserted-by":"publisher","first-page":"5179","DOI":"10.1021\/ja00124a002","volume":"117","author":"WD Cornell","year":"1995","unstructured":"Cornell WD, Cieplak P, Bayly CI et al (1995) A Second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117:5179\u20135197. doi: 10.1021\/ja00124a002","journal-title":"J Am Chem Soc"},{"key":"7_CR44","doi-asserted-by":"publisher","first-page":"e8140","DOI":"10.1371\/journal.pone.0008140","volume":"4","author":"D Xu","year":"2009","unstructured":"Xu D, Zhang Y (2009) Generating triangulated macromolecular surfaces by Euclidean distance transform. PLoS One 4:e8140. doi: 10.1371\/journal.pone.0008140","journal-title":"PLoS One"},{"key":"7_CR45","doi-asserted-by":"publisher","first-page":"2605","DOI":"10.1016\/j.bpj.2012.04.029","volume":"102","author":"S Basu","year":"2012","unstructured":"Basu S, Bhattacharyya D, Banerjee R (2012) Self-complementarity within proteins: bridging the gap between binding and folding. Biophys J 102:2605\u20132614. doi: 10.1016\/j.bpj.2012.04.029","journal-title":"Biophys J"},{"key":"7_CR46","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1002\/jcc.1161","volume":"23","author":"W Rocchia","year":"2002","unstructured":"Rocchia W, Sridharan S, Nicholls A et al (2002) Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects. J Comput Chem 23:128\u2013137. doi: 10.1002\/jcc.1161","journal-title":"J Comput Chem"},{"key":"7_CR47","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1186\/2046-1682-5-9","volume":"5","author":"L Li","year":"2012","unstructured":"Li L, Li C, Sarkar S, et al. (2012) DelPhi: a comprehensive suite for DelPhi software and associated resources. BMC Biophys 5:9. doi: 10.1186\/2046-1682-5-9","journal-title":"BMC Biophys"},{"key":"7_CR48","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1002\/jcc.20084","volume":"25","author":"EF Pettersen","year":"2004","unstructured":"Pettersen EF, Goddard TD, Huang CC et al (2004) UCSF Chimera\u2013a visualization system for exploratory research and analysis. J Comput Chem 25:1605\u20131612. doi: 10.1002\/jcc.20084","journal-title":"J Comput Chem"},{"key":"7_CR49","doi-asserted-by":"publisher","first-page":"W68","DOI":"10.1093\/nar\/gkr316","volume":"39","author":"C Blanchet","year":"2011","unstructured":"Blanchet C, Pasi M, Zakrzewska K, Lavery R (2011) CURVES + web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures. Nucleic Acids Res 39:W68\u2013W73. doi: 10.1093\/nar\/gkr316","journal-title":"Nucleic Acids Res"},{"key":"7_CR50","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4612-5190-3","author":"W Saenger","year":"1984","unstructured":"Saenger W (1984) Principles of nucleic acid. Structure. doi: 10.1007\/978-1-4612-5190-3","journal-title":"Structure"},{"key":"7_CR51","doi-asserted-by":"publisher","first-page":"720","DOI":"10.1038\/326720a0","volume":"326","author":"LE Ulanovsky","year":"1987","unstructured":"Ulanovsky LE, Trifonov EN (1987) Estimation of wedge components in curved DNA. Nature 326:720\u2013722. doi: 10.1038\/326720a0","journal-title":"Nature"},{"key":"7_CR52","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1186\/1756-0500-7-83","volume":"7","author":"S Kailasam","year":"2014","unstructured":"Kailasam S, Bhattacharyya D, Bansal M et al (2014) Sequence dependent variations in RNA duplex are related to non-canonical hydrogen bond interactions in dinucleotide steps. BMC Res Notes 7:83. doi: 10.1186\/1756-0500-7-83","journal-title":"BMC Res Notes"},{"key":"7_CR53","first-page":"281","volume-title":"Nonredundant 3D structure datasets for RNA knowledge extraction and benchmarking","author":"NB Leontis","year":"2012","unstructured":"Leontis NB, Zirbel CL (2012) In: Leontis N, Westhof E (eds) Nonredundant 3D structure datasets for RNA knowledge extraction and benchmarking. Springer Berlin Heidelberg, Berlin, pp\u00a0281\u2013298t;\/bib>"},{"key":"7_CR54","doi-asserted-by":"publisher","first-page":"969","DOI":"10.1002\/bip.22331","volume":"99","author":"TE Cheatham","year":"2013","unstructured":"Cheatham TE, Case DA (2013) Twenty-five years of nucleic acid simulations. Biopolymers 99:969\u2013977. doi: 10.1002\/bip.22331","journal-title":"Biopolymers"},{"key":"7_CR55","doi-asserted-by":"crossref","first-page":"1392","DOI":"10.1016\/0006-291X(72)90867-4","volume":"48","author":"S Arnott","year":"1972","unstructured":"Arnott S, Hukins DW, Dover SD (1972) Optimised parameters for RNA double-helices. Biochem Biophys Res Commun 48:1392\u20131399","journal-title":"Biochem Biophys Res Commun"},{"key":"7_CR56","doi-asserted-by":"publisher","first-page":"1465","DOI":"10.1006\/jmbi.1998.2233","volume":"284","author":"CM Duarte","year":"1998","unstructured":"Duarte CM, Pyle AM (1998) Stepping through an RNA structure: A novel approach to conformational analysis. J Mol Biol 284:1465\u20131478. doi: 10.1006\/jmbi.1998.2233","journal-title":"J Mol Biol"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-016-0007-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s10822-016-0007-0\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-016-0007-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,6,25]],"date-time":"2017-06-25T04:37:43Z","timestamp":1498365463000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s10822-016-0007-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,1,19]]},"references-count":56,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2017,2]]}},"alternative-id":["7"],"URL":"https:\/\/doi.org\/10.1007\/s10822-016-0007-0","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"type":"print","value":"0920-654X"},{"type":"electronic","value":"1573-4951"}],"subject":[],"published":{"date-parts":[[2017,1,19]]}}}