-
1
-
-
0003788049
-
The RNA world: The nature of modern RNA suggests a prebiotic RNA
-
3rd edit Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY
-
Gesteland R.F., Cech T., and Atkins J.F. The RNA world: the nature of modern RNA suggests a prebiotic RNA Cold Spring Harbor Monograph Series 43 3rd edit 2006 Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY
-
(2006)
Cold Spring Harbor Monograph Series 43
-
-
Gesteland, R.F.1
Cech, T.2
Atkins, J.F.3
-
3
-
-
0011279547
-
Seven basic conformations of nucleic acid structural units
-
Kim S.H., Berman H.M., Seeman N.C., and Newton M.D. Seven basic conformations of nucleic acid structural units Acta Crystallogr., Sect. B: Struct. Crystallogr. Cryst. Chem. 29 1973 703 710
-
(1973)
Acta Crystallogr., Sect. B: Struct. Crystallogr. Cryst. Chem.
, vol.29
, pp. 703-710
-
-
Kim, S.H.1
Berman, H.M.2
Seeman, N.C.3
Newton, M.D.4
-
4
-
-
0032780417
-
A complete conformational map for RNA
-
DOI 10.1006/jmbi.1999.2958
-
Murthy V.L., Srinivasan R., Draper D.E., and Rose G.D. A complete conformational map for RNA J. Mol. Biol. 291 1999 313 327 (Pubitemid 29381430)
-
(1999)
Journal of Molecular Biology
, vol.291
, Issue.2
, pp. 313-327
-
-
Murthy, V.L.1
Srinivasan, R.2
Draper, D.E.3
Rose, G.D.4
-
5
-
-
33144475030
-
Statistical analysis of RNA backbone
-
DOI 10.1109/TCBB.2006.13
-
Hershkovitz E., Sapiro G., Tannenbaum A., and Williams L.D. Statistical analysis of RNA backbone IEEE/ACM Trans. Comput. Biol. Bioinform. 3 2006 33 46 (Pubitemid 43269825)
-
(2006)
IEEE/ACM Transactions on Computational Biology and Bioinformatics
, vol.3
, Issue.1
, pp. 33-46
-
-
Hershkovitz, E.1
Sapiro, G.2
Tannenbaum, A.3
Williams, L.D.4
-
7
-
-
0344702704
-
RNA backbone is rotameric
-
DOI 10.1073/pnas.1835769100
-
Murray L.J.W., Arendall r., Bryan W., Richardson D.C., and Richardson J.S. RNA backbone is rotameric Proc. Natl Acad. Sci. USA 100 2003 13904 13909 (Pubitemid 37499164)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.SUPPL. 2
, pp. 13904-13909
-
-
Murray, L.J.W.1
Arendall III, W.B.2
Richardson, D.C.3
Richardson, J.S.4
-
8
-
-
40449091092
-
RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)
-
DOI 10.1261/rna.657708
-
Richardson J.S., Schneider B., Murray L.W., Kapral G.J., Immormino R.M., Headd J.J. RNA Ontology Consortium RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution) RNA 14 2008 465 481 (Pubitemid 351397812)
-
(2008)
RNA
, vol.14
, Issue.3
, pp. 465-481
-
-
Richardson, J.S.1
Schneider, B.2
Murray, L.W.3
Kapral, G.J.4
Immormino, R.M.5
Headd, J.J.6
Richardson, D.C.7
Ham, D.8
Hershkovits, E.9
Williams, L.D.10
Keating, K.S.11
Pyle, A.M.12
Micallef, D.13
Westbrook, J.14
Berman, H.M.15
-
9
-
-
0035010211
-
Geometric nomenclature and classification of RNA base pairs
-
DOI 10.1017/S1355838201002515
-
Leontis N.B., and Westhof E. Geometric nomenclature and classification of RNA base pairs RNA 7 2001 499 512 (Pubitemid 32416808)
-
(2001)
RNA
, vol.7
, Issue.4
, pp. 499-512
-
-
Leontis, N.B.1
Westhof, E.2
-
10
-
-
17844366343
-
Recurrent structural RNA motifs, Isostericity matrices and sequence alignments
-
DOI 10.1093/nar/gki535
-
Lescoute A., Leontis N.B., Massire C., and Westhof E. Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments Nucleic Acids Res. 33 2005 2395 2409 (Pubitemid 41511259)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.8
, pp. 2395-2409
-
-
Lescoute Aurelie1
Leontis, N.B.2
Massire, C.3
Westhof, E.4
-
12
-
-
0014885326
-
Studies on the conformation of amino acids. XI. Analysis of the observed side group conformation in proteins
-
Chandrasekaran R., and Ramachandran G.N. Studies on the conformation of amino acids. XI. Analysis of the observed side group conformation in proteins Int. J. Protein Res. 2 1970 223 233
-
(1970)
Int. J. Protein Res.
, vol.2
, pp. 223-233
-
-
Chandrasekaran, R.1
Ramachandran, G.N.2
-
13
-
-
0027160197
-
Backbone-dependent rotamer library for proteins. Application to side-chain prediction
-
DOI 10.1006/jmbi.1993.1170
-
Dunbrack R.L. Jr, and Karplus M. Backbone-dependent rotamer library for proteins. Application to side-chain prediction J. Mol. Biol. 230 1993 543 574 (Pubitemid 23161363)
-
(1993)
Journal of Molecular Biology
, vol.230
, Issue.2
, pp. 543-574
-
-
Dunbrack Jr., R.L.1
Karplus, M.2
-
14
-
-
0028429178
-
Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains
-
Dunbrack R.L. Jr, and Karplus M. Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains Nat. Struct. Biol. 1 1994 334 340
-
(1994)
Nat. Struct. Biol.
, vol.1
, pp. 334-340
-
-
Dunbrack Jr., R.L.1
Karplus, M.2
-
15
-
-
0034663722
-
The penultimate rotamer library
-
DOI 10.1002/1097-0134(20000815)40:3<389::AID-PROT50>3.0.CO;2-2
-
Lovell S.C., Word J.M., Richardson J.S., and Richardson D.C. The penultimate rotamer library Proteins: Struct., Funct., Genet. 40 2000 389 408 (Pubitemid 30624447)
-
(2000)
Proteins: Structure, Function and Genetics
, vol.40
, Issue.3
, pp. 389-408
-
-
Lovell, S.C.1
Word, J.M.2
Richardson, J.S.3
Richardson, D.C.4
-
16
-
-
0023155210
-
Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes
-
DOI 10.1016/0022-2836(87)90358-5
-
Ponder J.W., and Richards F.M. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes J. Mol. Biol. 193 1987 775 791 (Pubitemid 17020078)
-
(1987)
Journal of Molecular Biology
, vol.193
, Issue.4
, pp. 775-791
-
-
Ponder, J.W.1
Richards, F.M.2
-
17
-
-
0036667731
-
Rotamer libraries in the 21st century
-
Dunbrack R.L. Jr Rotamer libraries in the 21st century Curr. Opin. Struct. Biol. 12 2002 431 440
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 431-440
-
-
Dunbrack Jr., R.L.1
-
18
-
-
1342310514
-
Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library
-
DOI 10.1110/ps.03250104
-
Peterson R.W., Dutton P.L., and Wand A.J. Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library Protein Sci. 13 2004 735 751 (Pubitemid 38252571)
-
(2004)
Protein Science
, vol.13
, Issue.3
, pp. 735-751
-
-
Peterson, R.W.1
Dutton, P.L.2
Wand, A.J.3
-
19
-
-
0035838974
-
Extending the accuracy limits of prediction for side-chain conformations
-
DOI 10.1006/jmbi.2001.4865
-
Xiang Z., and Honig B. Extending the accuracy limits of prediction for side-chain conformations J. Mol. Biol. 311 2001 421 430 (Pubitemid 32744551)
-
(2001)
Journal of Molecular Biology
, vol.311
, Issue.2
, pp. 421-430
-
-
Xiang, Z.1
Honig, B.2
-
20
-
-
0027208112
-
Rotamers: To be or not to be? An analysis of amino acid side-chain conformations in globular proteins
-
DOI 10.1006/jmbi.1993.1172
-
Schrauber H., Eisenhaber F., and Argos P. Rotamers: to be or not to be? An analysis of amino acid side-chain conformations in globular proteins J. Mol. Biol. 230 1993 592 612 (Pubitemid 23161365)
-
(1993)
Journal of Molecular Biology
, vol.230
, Issue.2
, pp. 592-612
-
-
Schrauber, H.1
Eisenhaber, F.2
Argos, P.3
-
21
-
-
0030623575
-
All in one: A highly detailed rotamer library improves both accuracy and speed in the modelling of sidechains by dead-end elimination
-
De Maeyer M., Desmet J., and Lasters I. All in one: a highly detailed rotamer library improves both accuracy and speed in the modelling of sidechains by dead-end elimination Folding Des. 2 1997 53 66 (Pubitemid 127740451)
-
(1997)
Folding and Design
, vol.2
, Issue.1
, pp. 53-66
-
-
De Maeyer, M.1
Desmet, J.2
Lasters, I.3
-
22
-
-
3242886389
-
MOLPROBITY: Structure validation and all-atom contact analysis for nucleic acids and their complexes
-
Davis I.W., Murray L.W., Richardson J.S., and Richardson D.C. MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes Nucleic Acids Res. 32 2004 W615 619
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 615-619
-
-
Davis, I.W.1
Murray, L.W.2
Richardson, J.S.3
Richardson, D.C.4
-
23
-
-
77952352777
-
Semiautomated model building for RNA crystallography using a directed rotameric approach
-
Keating K.S., and Pyle A.M. Semiautomated model building for RNA crystallography using a directed rotameric approach Proc. Natl Acad. Sci. USA 107 2010 8177 8182
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 8177-8182
-
-
Keating, K.S.1
Pyle, A.M.2
-
24
-
-
34147104014
-
Bridging the gap in RNA structure prediction
-
DOI 10.1016/j.sbi.2007.03.001, PII S0959440X07000310, Theory and Simulation / Mecromolecular Assemblages
-
Shapiro B.A., Yingling Y.G., Kasprzak W., and Bindewald E. Bridging the gap in RNA structure prediction Curr. Opin. Struct. Biol. 17 2007 157 165 (Pubitemid 46575248)
-
(2007)
Current Opinion in Structural Biology
, vol.17
, Issue.2
, pp. 157-165
-
-
Shapiro, B.A.1
Yingling, Y.G.2
Kasprzak, W.3
Bindewald, E.4
-
25
-
-
44149101971
-
Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms
-
DOI 10.1261/rna.894608
-
Ding F., Sharma S., Chalasani P., Demidov V.V., Broude N.E., and Dokholyan N.V. Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms RNA 14 2008 1164 1173 (Pubitemid 351717496)
-
(2008)
RNA
, vol.14
, Issue.6
, pp. 1164-1173
-
-
Ding, F.1
Sharma, S.2
Chalasani, P.3
Demidov, V.V.4
Broude, N.E.5
Dokholyan, N.V.6
-
26
-
-
50549096615
-
IFoldRNA: Three-dimensional RNA structure prediction and folding
-
Sharma S., Ding F., and Dokholyan N.V. iFoldRNA: three-dimensional RNA structure prediction and folding Bioinformatics 24 2008 1951 1952
-
(2008)
Bioinformatics
, vol.24
, pp. 1951-1952
-
-
Sharma, S.1
Ding, F.2
Dokholyan, N.V.3
-
27
-
-
58249111738
-
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters
-
Jonikas M.A., Radmer R.J., Laederach A., Das R., Pearlman S., Herschlag D., and Altman R.B. Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters RNA 15 2009 189 199
-
(2009)
RNA
, vol.15
, pp. 189-199
-
-
Jonikas, M.A.1
Radmer, R.J.2
Laederach, A.3
Das, R.4
Pearlman, S.5
Herschlag, D.6
Altman, R.B.7
-
28
-
-
75849116392
-
Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models
-
Jonikas M.A., Radmer R.J., and Altman R.B. Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models Bioinformatics 25 2009 3259 3266
-
(2009)
Bioinformatics
, vol.25
, pp. 3259-3266
-
-
Jonikas, M.A.1
Radmer, R.J.2
Altman, R.B.3
-
29
-
-
0026077710
-
The combination of symbolic and numerical computation for three-dimensional modeling of RNA
-
Major F., Turcotte M., Gautheret D., Lapalme G., Fillion E., and Cedergren R. The combination of symbolic and numerical computation for three-dimensional modeling of RNA Science 253 1991 1255 1260 (Pubitemid 21917270)
-
(1991)
Science
, vol.253
, Issue.5025
, pp. 1255-1260
-
-
Major, F.1
Turcotte, M.2
Gautheret, D.3
Lapalme, G.4
Fillion, E.5
Cedergren, R.6
-
30
-
-
40449139010
-
The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data
-
DOI 10.1038/nature06684, PII NATURE06684
-
Parisien M., and Major F. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data Nature 452 2008 51 55 (Pubitemid 351355097)
-
(2008)
Nature
, vol.452
, Issue.7183
, pp. 51-55
-
-
Parisien, M.1
Major, F.2
-
32
-
-
0032545158
-
Stepping through an RNA structure: A novel approach to conformational analysis
-
DOI 10.1006/jmbi.1998.2233
-
Duarte C.M., and Pyle A.M. Stepping through an RNA structure: a novel approach to conformational analysis J. Mol. Biol. 284 1998 1465 1478 (Pubitemid 28566081)
-
(1998)
Journal of Molecular Biology
, vol.284
, Issue.5
, pp. 1465-1478
-
-
Duarte, C.M.1
Pyle, A.M.2
-
33
-
-
34548401692
-
Evaluating and Learning from RNA Pseudotorsional Space: Quantitative Validation of a Reduced Representation for RNA Structure
-
DOI 10.1016/j.jmb.2007.06.058, PII S0022283607008509
-
Wadley L.M., Keating K.S., Duarte C.M., and Pyle A.M. Evaluating and learning from RNA pseudotorsional space: quantitative validation of a reduced representation for RNA structure J. Mol. Biol. 372 2007 942 957 (Pubitemid 47368342)
-
(2007)
Journal of Molecular Biology
, vol.372
, Issue.4
, pp. 942-957
-
-
Wadley, L.M.1
Keating, K.S.2
Duarte, C.M.3
Pyle, A.M.4
-
35
-
-
0344012516
-
RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space
-
DOI 10.1093/nar/gkg682
-
Duarte C.M., Wadley L.M., and Pyle A.M. RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space Nucleic Acids Res. 31 2003 4755 4761 (Pubitemid 37441838)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.16
, pp. 4755-4761
-
-
Duarte, C.M.1
Wadley, L.M.2
Pyle, A.M.3
-
36
-
-
13544255744
-
The identification of novel RNA structural motifs using COMPADRES: An automated approach to structural discovery
-
DOI 10.1093/nar/gkh1002
-
Wadley L.M., and Pyle A.M. The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery Nucleic Acids Res. 32 2004 6650 6659 (Pubitemid 40220377)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.22
, pp. 6650-6659
-
-
Wadley, L.M.1
Pyle, A.M.2
-
37
-
-
70349149051
-
New metrics for comparing and assessing discrepancies between RNA 3D structures and models
-
Parisien M., Cruz J.A., Westhof E., and Major F. New metrics for comparing and assessing discrepancies between RNA 3D structures and models RNA 15 2009 1875 1885
-
(2009)
RNA
, vol.15
, pp. 1875-1885
-
-
Parisien, M.1
Cruz, J.A.2
Westhof, E.3
Major, F.4
-
38
-
-
77953784130
-
Computational approaches to 3D modeling of RNA
-
Laing C., and Schlick T. Computational approaches to 3D modeling of RNA J. Phys. Condens. Matter. 22 2010 283101
-
(2010)
J. Phys. Condens. Matter.
, vol.22
, pp. 283101
-
-
Laing, C.1
Schlick, T.2
-
39
-
-
0027520909
-
Modeling the three-dimensional structure of RNA using discrete nucleotide conformational sets
-
DOI 10.1006/jmbi.1993.1104
-
Gautheret D., Major F., and Cedergren R. Modeling the three-dimensional structure of RNA using discrete nucleotide conformational sets J. Mol. Biol. 229 1993 1049 1064 (Pubitemid 23091820)
-
(1993)
Journal of Molecular Biology
, vol.229
, Issue.4
, pp. 1049-1064
-
-
Gautheret, D.1
Major, F.2
Cedergren, R.3
-
41
-
-
77953648210
-
On the significance of an RNA tertiary structure prediction
-
Hajdin C.E., Ding F., Dokholyan N.V., and Weeks K.M. On the significance of an RNA tertiary structure prediction RNA 16 2010 1340 1349
-
(2010)
RNA
, vol.16
, pp. 1340-1349
-
-
Hajdin, C.E.1
Ding, F.2
Dokholyan, N.V.3
Weeks, K.M.4
-
42
-
-
22044438679
-
Describing RNA structure by libraries of clustered nucleotide doublets
-
DOI 10.1016/j.jmb.2005.06.024, PII S0022283605006741
-
Sykes M.T., and Levitt M. Describing RNA structure by libraries of clustered nucleotide doublets J. Mol. Biol. 351 2005 26 38 (Pubitemid 40967053)
-
(2005)
Journal of Molecular Biology
, vol.351
, Issue.1
, pp. 26-38
-
-
Sykes, M.T.1
Levitt, M.2
-
43
-
-
0033613812
-
Visualizing and quantifying molecular goodness-of-fit: Small-probe contact dots with explicit hydrogen atoms
-
DOI 10.1006/jmbi.1998.2400
-
Word J.M., Lovell S.C., LaBean T.H., Taylor H.C., Zalis M.E., and Presley B.K. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms J. Mol. Biol. 285 1999 1711 1733 (Pubitemid 29060466)
-
(1999)
Journal of Molecular Biology
, vol.285
, Issue.4
, pp. 1711-1733
-
-
Word, J.M.1
Lovell, S.C.2
Labean, T.H.3
Taylor, H.C.4
Zalis, M.E.5
Presley, B.K.6
Richardson, J.S.7
Richardson, D.C.8
-
44
-
-
34547592557
-
MolProbity: All-atom contacts and structure validation for proteins and nucleic acids
-
Davis I.W., Leaver-Fay A., Chen V.B., Block J.N., Kapral G.J., and Wang X. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids Nucleic Acids Res. 35 2007 W375 W383
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Davis, I.W.1
Leaver-Fay, A.2
Chen, V.B.3
Block, J.N.4
Kapral, G.J.5
Wang, X.6
|