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An all-atom empirical energy function for the simulation of nucleic acids

https://doi.org/10.1021/ja00153a017
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inferred← citeshttps://doi.org/10.2139/ssrn.4790019openalex-extracted
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inferred← citeshttps://doi.org/10.1002/(sici)1096-987x(19970130)18:2<221::aid-jcc7>3.0.co;2-xopenalex-snapshot
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inferred← citeshttps://doi.org/10.1002/(sici)1096-987x(19970715)18:9<1136::aid-jcc3>3.0.co;2-sopenalex-snapshot
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inferred← citeshttps://doi.org/10.1002/(sici)1096-987x(199710)18:13<1632::aid-jcc5>3.0.co;2-sopenalex-snapshot
Advancing beyond the atom-centered model in additive and nonadditive molecular mechanics
inferred← citeshttps://doi.org/10.1002/(sici)1096-987x(199802)19:3<334::aid-jcc7>3.0.co;2-uopenalex-snapshot
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inferred← citeshttps://doi.org/10.1002/(sici)1096-987x(19990415)20:5<531::aid-jcc5>3.0.co;2-3openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/(sici)1096-987x(199905)20:7<720::aid-jcc7>3.0.co;2-xopenalex-snapshot
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inferred← citeshttps://doi.org/10.1002/(sici)1096-987x(199905)20:7<730::aid-jcc8>3.0.co;2-topenalex-snapshot
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inferred← citeshttps://doi.org/10.1002/(sici)1096-987x(199906)20:8<877::aid-jcc12>3.0.co;2-oopenalex-snapshot
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inferred← citeshttps://doi.org/10.1002/(sici)1096-987x(20000130)21:2<105::aid-jcc3>3.0.co;2-popenalex-snapshot
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inferred← citeshttps://doi.org/10.1002/(sici)1096-987x(20000130)21:2<86::aid-jcc2>3.0.co;2-gopenalex-snapshot
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inferred← citeshttps://doi.org/10.1002/(sici)1097-0134(19980201)30:2<113::aid-prot2>3.0.co;2-oopenalex-snapshot
Structure prediction of a complex between the chromosomal protein HMG-D and DNA
inferred← citeshttps://doi.org/10.1002/(sici)1097-0134(19980601)31:4<417::aid-prot8>3.0.co;2-eopenalex-snapshot
Interaction of human SRY protein with DNA: A molecular dynamics study
inferred← citeshttps://doi.org/10.1002/(sici)1097-0134(19980815)32:3<362::aid-prot11>3.0.co;2-7openalex-snapshot
Engineering an Mg2 site to replace a structurally conserved arginine in the catalytic center of histidyl‐tRNA synthetase by computer experiments
inferred← citeshttps://doi.org/10.1002/(sici)1097-0134(19990401)35:1<101::aid-prot10>3.0.co;2-5openalex-snapshot
Effect of G40R mutation on the binding of human SRY protein to DNA: A molecular dynamics view
inferred← citeshttps://doi.org/10.1002/(sici)1097-0282(199612)39:6<765::aid-bip3>3.0.co;2-topenalex-snapshot
Influence of adjacent bases on the stacking-unstacking process of single-stranded oligonucleotides
inferred← citeshttps://doi.org/10.1002/(sici)1097-0282(1999)52:1<1::aid-bip1>3.0.co;2-wopenalex-snapshot
Transfer RNA recognition by aminoacyl-tRNA synthetases
inferred← citeshttps://doi.org/10.1002/(sici)1097-461x(1999)73:2<237::aid-qua17>3.0.co;2-wopenalex-snapshot
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inferred← citeshttps://doi.org/10.1002/0470027320.s4204openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/0470845015.cda022openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/0470845015.cfa007openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/0470845015.cma022openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/0470845015.cma023openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/0470845015.cn0080openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/0470845015.cna010openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/0470845015.cna011openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/0470845015.cpa029openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/0470845015.cpa033fopenalex-snapshot
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inferred← citeshttps://doi.org/10.1002/0471142700.nc0709s05openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/0471142700.nc0709s55openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/0471142700.nc0710s06openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/0471142700.nc0710s56openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/1096-987x(200010)21:13<1132::aid-jcc2>3.0.co;2-5openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/1096-987x(200103)22:4<457::aid-jcc1016>3.0.co;2-hopenalex-snapshot
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inferred← citeshttps://doi.org/10.1002/1097-0282(2000)56:4<232::aid-bip10037>3.0.co;2-hopenalex-snapshot
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inferred← citeshttps://doi.org/10.1002/1097-0282(2000)56:4<257::aid-bip10029>3.0.co;2-wopenalex-snapshot
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inferred← citeshttps://doi.org/10.1002/3527600434.eap665openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9780470027318.a9193openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/adem.202402289openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/adfm.202519573openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/bip.10583openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/bip.20147openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/bip.22189openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/chem.19970030610openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/chem.201404016openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/cphc.200400542openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/cphc.200500510openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/cphc.200900541openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/cphc.202200175openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/hlca.19980810544openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.10260openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.1137openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.1166openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.20082openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.20090openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.20281openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.20317openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.20386openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.20453openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.20474openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.20643openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.20844openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.20974openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.21004openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.21006openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.21040openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.21287openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.21367openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.21442openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.22946openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.23207openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.23247openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.23422openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.23808openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.24043openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.70351openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jmr.980openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.5560070918openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/prot.1159openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/prot.20137openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/prot.20540openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/prot.22563openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/prot.24023openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/prot.24158openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/prot.25271openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/qua.10114openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/qua.20417openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/qua.21191openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/qua.22957openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/smll.202204408openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/wcms.1142openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/wcms.1346openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/wcms.1655openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/wcms.70024openalex-snapshot
Current Advances in Genome Modeling Across Length Scales
inferred← citeshttps://doi.org/10.1002/wcms.74openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/wrna.1396openalex-snapshot
Advances in RNA molecular dynamics: a simulator's guide to RNA force fields
inferred← citeshttps://doi.org/10.1002/wrna.1422openalex-snapshot
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inferred← citeshttps://doi.org/10.1006/jmbi.1997.1292openalex-snapshot
The crystal structure of a parallel-stranded guanine tetraplex at 0.95Å resolution
inferred← citeshttps://doi.org/10.1006/jmbi.1998.1833openalex-snapshot
On the potential role of the amino nitrogen atom as a hydrogen bond acceptor in macromolecules
inferred← citeshttps://doi.org/10.1006/jmbi.1998.2139openalex-snapshot
Conformational analysis of GpA and GpAp in aqueous solution by molecular dynamics and statistical methods 1 1Edited by A. R. Fersht
inferred← citeshttps://doi.org/10.1006/jmbi.1998.2486openalex-snapshot
Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation 1 1Edited by B. Honig
inferred← citeshttps://doi.org/10.1006/jmbi.1999.3131openalex-snapshot
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inferred← citeshttps://doi.org/10.1006/jmbi.2000.3894openalex-snapshot
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inferred← citeshttps://doi.org/10.1006/jmbi.2000.4173openalex-snapshot
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inferred← citeshttps://doi.org/10.1006/jmbi.2000.4360openalex-snapshot
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inferred← citeshttps://doi.org/10.1006/jmbi.2001.4642openalex-snapshot
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inferred← citeshttps://doi.org/10.1006/jtbi.2003.3108openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/0-306-46934-0_4openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/1-4020-3286-2_26openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/128_2011_164openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/3-540-35284-8_17openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-0-387-68372-0_2openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-4020-4851-3_3openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-4020-4851-3_8openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-4020-6330-5_18openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-4419-6351-2_13openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-4615-1223-3_2openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-4615-5903-0_20openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-4684-8580-6_2openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-4939-1465-4_3openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-4939-9446-5_5openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-59745-177-2_4openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-59745-398-1_32openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-3-030-05600-1_6openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-3-031-70499-4_5openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-3-0348-7907-1_36openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-3-319-67132-1_6openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-3-642-46879-7_4openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-94-010-0191-5_9openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-94-010-0864-8_16openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-94-011-4225-0_12openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-94-011-4225-0_9openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-94-011-4554-1_6openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-94-017-1120-3_1openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-94-017-1120-3_2openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-94-017-1120-3_9openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-981-19-3092-8_1openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-981-96-4154-3_15openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-981-99-2079-2_10openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/bf00200432openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/bfb0095349openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s00023-003-0936-8openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s00044-014-1182-yopenalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s00214-005-0024-xopenalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s00214-005-0672-xopenalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s00214-006-0170-9openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s00214-009-0592-2openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s00214-011-0931-yopenalex-snapshot
An atomistic model for simulations of nilotinib and nilotinib/kinase binding
inferred← citeshttps://doi.org/10.1007/s00214-015-1671-1openalex-snapshot
Development of force field parameters for cyclopentane-modified peptide nucleic acids
inferred← citeshttps://doi.org/10.1007/s00214-015-1739-yopenalex-snapshot
Transferable kriging machine learning models for the multipolar electrostatics of helical deca-alanine
inferred← citeshttps://doi.org/10.1007/s00249-004-0410-7openalex-snapshot
A molecular dynamics simulation study of polyamine? and sodium?DNA. Interplay between polyamine binding and DNA structure
inferred← citeshttps://doi.org/10.1007/s00249-004-0448-6openalex-snapshot
Validation of the 53A6 GROMOS force field
inferred← citeshttps://doi.org/10.1007/s00249-011-0700-9openalex-snapshot
Definition and testing of the GROMOS force-field versions 54A7 and 54B7
inferred← citeshttps://doi.org/10.1007/s002490050189openalex-snapshot
Structural and dynamic differences of the estrogen receptor DNA-binding domain, binding as a dimer and as a monomer to DNA: molecular dynamics simulation studies
inferred← citeshttps://doi.org/10.1007/s002490050224openalex-snapshot
Structure, force, and energy of a double-stranded DNA oligonucleotide under tensile loads
inferred← citeshttps://doi.org/10.1007/s00894-005-0255-8openalex-snapshot
Force field impact and spin-probe modeling in molecular dynamics simulations of spin-labeled T4 lysozyme
inferred← citeshttps://doi.org/10.1007/s00894-009-0474-5openalex-snapshot
A butterfly effect: highly insecticidal resistance caused by only a conservative residue mutated of drosophila melanogaster acetylcholinesterase
inferred← citeshttps://doi.org/10.1007/s00894-012-1638-2openalex-snapshot
Computational design of a CNT carrier for a high affinity bispecific anti-HER2 antibody based on trastuzumab and pertuzumab Fabs
inferred← citeshttps://doi.org/10.1007/s00894-016-3033-xopenalex-snapshot
Gibbs ensemble Monte Carlo simulation using an optimized potential model: pure acetic acid and a mixture of it with ethylene
inferred← citeshttps://doi.org/10.1007/s00894-017-3364-2openalex-snapshot
Prediction of self-assemblies of sodium dodecyl sulfate and fragrance additives using coarse-grained force fields
inferred← citeshttps://doi.org/10.1007/s00894-021-04731-2openalex-snapshot
Partial charges for molecular-mechanical models of heterocyclic compounds: pyridine nitrogen
inferred← citeshttps://doi.org/10.1007/s10409-005-0027-9openalex-snapshot
Molecular dynamics simulation of peeling a DNA molecule on substrate
inferred← citeshttps://doi.org/10.1007/s10822-009-9287-yopenalex-snapshot
The multi-copy simultaneous search methodology: a fundamental tool for structure-based drug design
inferred← citeshttps://doi.org/10.1007/s10822-021-00407-4openalex-snapshot
Precise force-field-based calculations of octanol-water partition coefficients for the SAMPL7 molecules
inferred← citeshttps://doi.org/10.1007/s10822-021-00415-4openalex-snapshot
Predicting octanol/water partition coefficients using molecular simulation for the SAMPL7 challenge: comparing the use of neat and water saturated 1-octanol
inferred← citeshttps://doi.org/10.1007/s10858-004-5430-1openalex-snapshot
Validation of the GROMOS force-field parameter set 45A3 against nuclear magnetic resonance data of hen egg lysozyme
inferred← citeshttps://doi.org/10.1007/s11051-012-0936-zopenalex-snapshot
Molecular dynamics simulation of β-sheet formation in self-assembled peptide amphiphile fibers
inferred← citeshttps://doi.org/10.1007/s11095-007-9506-yopenalex-snapshot
Structural Behaviour of 2-Hydroxypropyl-β-Cyclodextrin in Water: Molecular Dynamics Simulation Studies
inferred← citeshttps://doi.org/10.1007/s11426-012-4749-9openalex-snapshot
Optimization of CHARMM force field parameters for the chalcone fragment
inferred← citeshttps://doi.org/10.1007/s11705-016-1572-4openalex-snapshot
Validation of polarizable force field parameters for nucleic acids by inter-molecular interactions
inferred← citeshttps://doi.org/10.1007/s12039-017-1263-9openalex-snapshot
Microstructures and their lifetimes in acetamide/electrolyte deep eutectics: anion dependence
inferred← citeshttps://doi.org/10.1007/s13205-023-03821-7openalex-snapshot
Enhancing temozolomide antiglioma response by inhibiting O6-methylguanine-DNA methyltransferase with selected phytochemicals: in silico and in vitro approach
inferred← citeshttps://doi.org/10.1007/s43630-022-00187-2openalex-snapshot
Comparing ultrafast excited state quenching of flavin 1,N6-ethenoadenine dinucleotide and flavin adenine dinucleotide by optical spectroscopy and DFT calculations
inferred← citeshttps://doi.org/10.1016/0009-2614(96)00537-4openalex-snapshot
Ability of empirical potentials (AMBER, CHARMM, CVFF, OPLS, Poltev) and semi-empirical quantum chemical methods (AM1, MNDO/M, PM3) to describe H-bonding in DNA base pairs; comparison with ab initio results
inferred← citeshttps://doi.org/10.1016/b0-08-045044-x/00268-6openalex-snapshot
Applications of Molecular Dynamics Simulations in Drug Design
inferred← citeshttps://doi.org/10.1016/b978-0-12-386485-7.00005-3openalex-snapshot
Coarse-grained Representation of Protein Flexibility. Foundations, Successes, and Shortcomings
inferred← citeshttps://doi.org/10.1016/b978-0-12-813641-6.00001-7openalex-snapshot
Molecular Perspective of Gas–Liquid Interfaces
inferred← citeshttps://doi.org/10.1016/b978-0-12-821978-2.00138-0openalex-snapshot
Quantum Chemical and Informatics-Based Approaches for Probing Biomolecular Systems Toxicology
inferred← citeshttps://doi.org/10.1016/b978-0-12-823789-2.00001-7openalex-snapshot
Modeling and simulation of graphene-based composites
inferred← citeshttps://doi.org/10.1016/b978-0-323-95917-9.00019-5openalex-snapshot
Molecule scale
inferred← citeshttps://doi.org/10.1016/b978-0-443-26596-9.00013-2openalex-snapshot
Biomolecular force fields: advances in nonstandard amino acid and nucleic acid development
inferred← citeshttps://doi.org/10.1016/b978-0-444-53349-4.00236-3openalex-snapshot
Viral Packaging of Nucleic Acids
inferred← citeshttps://doi.org/10.1016/b978-012492543-4/50008-8openalex-snapshot
The Nucleic Acids
inferred← citeshttps://doi.org/10.1016/b978-044452220-7/50071-xopenalex-snapshot
Computer simulations of DNA stretching
inferred← citeshttps://doi.org/10.1016/bs.abl.2019.09.002openalex-snapshot
Multiscale (re)modeling of lipid bilayer membranes
inferred← citeshttps://doi.org/10.1016/bs.armc.2020.04.002openalex-snapshot
Molecular dynamics simulations of G-quadruplexes: The basic principles and their application to folding and ligand binding
inferred← citeshttps://doi.org/10.1016/j.actbio.2019.10.045openalex-snapshot
Peptide science: A “rule model” for new generations of peptidomimetics
inferred← citeshttps://doi.org/10.1016/j.bbagen.2014.08.004openalex-snapshot
CHARMM additive and polarizable force fields for biophysics and computer-aided drug design
inferred← citeshttps://doi.org/10.1016/j.bbagen.2014.09.018openalex-snapshot
All-atom crystal simulations of DNA and RNA duplexes
inferred← citeshttps://doi.org/10.1016/j.bbagen.2020.129614openalex-snapshot
Proton transfer in the D-channel of cytochrome c oxidase modeled by a transition network approach
inferred← citeshttps://doi.org/10.1016/j.bbamem.2015.12.033openalex-snapshot
Force Field Development for Lipid Membrane Simulations
inferred← citeshttps://doi.org/10.1016/j.bpj.2015.11.029openalex-snapshot
Direct Calculation of Protein Fitness Landscapes through Computational Protein Design
inferred← citeshttps://doi.org/10.1016/j.bpj.2022.12.022openalex-snapshot
The development of nucleic acids force fields: From an unchallenged past to a competitive future
inferred← citeshttps://doi.org/10.1016/j.cclet.2007.07.029openalex-snapshot
An investigation of crambin and BPTI based on ABEEM/MM model
inferred← citeshttps://doi.org/10.1016/j.ces.2011.11.020openalex-snapshot
Effect of water content on microstructures and oxygen permeation in PSiMA–IPN–PMPC hydrogel: a molecular simulation study
inferred← citeshttps://doi.org/10.1016/j.chemphys.2009.04.022openalex-snapshot
Theoretical studies of uracil–(H2O)n (n=1–7) clusters by ab initio and ABEEMσπ/MM fluctuating charge model
inferred← citeshttps://doi.org/10.1016/j.chemphys.2026.113426openalex-snapshot
Solvation behavior and hydrogen bond properties of DNA base pairs and their interactions with Mg2+, Ca2+, and Zn2+ ions: a model comparison study
inferred← citeshttps://doi.org/10.1016/j.chempr.2018.09.015openalex-snapshot
Modeling, Simulations, and Bioinformatics at the Service of RNA Structure
inferred← citeshttps://doi.org/10.1016/j.chphi.2023.100313openalex-snapshot
Effect of Water Models on The Stability of RNA: Role of Counter-Ions
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