-
1
-
-
33646799407
-
Multiscale modeling of macromolecular conformational changes combining concepts from rigidity and elastic network theory
-
Ahmed A, Gohlke H. 2006. Multiscale modeling of macromolecular conformational changes combining concepts from rigidity and elastic network theory. Proteins 63: 1038-1051.
-
(2006)
Proteins
, vol.63
, pp. 1038-1051
-
-
Ahmed, A.1
Gohlke, H.2
-
2
-
-
53549133573
-
Protein flexibility and mobility in structure-based drug design
-
Ahmed A, Kazemi S, Gohlke H. 2007. Protein flexibility and mobility in structure-based drug design. Front. Drug Des. Discov. 3: 455-476.
-
(2007)
Front. Drug Des. Discov
, vol.3
, pp. 455-476
-
-
Ahmed, A.1
Kazemi, S.2
Gohlke, H.3
-
3
-
-
24744434584
-
Dynamics-based amplification of RNA function and its characterization by using NMR spectroscopy
-
Al-Hashimi HM. 2005. Dynamics-based amplification of RNA function and its characterization by using NMR spectroscopy. ChemBioChem 6: 1506-1519.
-
(2005)
Chembiochem
, vol.6
, pp. 1506-1519
-
-
Al-Hashimi, H.M.1
-
4
-
-
0036290269
-
Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings
-
Al-Hashimi HM, Gosser Y, Gorin A, Hu W, Majumdar A, Patel DJ. 2002. Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings. J. Mol. Biol. 315: 95-102.
-
(2002)
J. Mol. Biol
, vol.315
, pp. 95-102
-
-
Al-Hashimi, H.M.1
Gosser, Y.2
Gorin, A.3
Hu, W.4
Majumdar, A.5
Patel, D.J.6
-
5
-
-
0038206733
-
Mg2{thorn}-induced variations in the conformation and dynamics of HIV-1 TAR RNA probed using NMR residual dipolar couplings
-
Al-Hashimi HM, Pitt SW, Majumdar A, Xu W, Patel DJ. 2003. Mg2{thorn}-induced variations in the conformation and dynamics of HIV-1 TAR RNA probed using NMR residual dipolar couplings. J. Mol. Biol. 329: 867-873.
-
(2003)
J. Mol. Biol
, vol.329
, pp. 867-873
-
-
Al-Hashimi, H.M.1
Pitt, S.W.2
Majumdar, A.3
Xu, W.4
Patel, D.J.5
-
7
-
-
0035132230
-
Anisotropy of fluctuation dynamics of proteins with an elastic net-work model
-
Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I. 2001. Anisotropy of fluctuation dynamics of proteins with an elastic net-work model. Biophys. J. 80: 505-515.
-
(2001)
Biophys. J
, vol.80
, pp. 505-515
-
-
Atilgan, A.R.1
Durell, S.R.2
Jernigan, R.L.3
Demirel, M.C.4
Keskin, O.5
Bahar, I.6
-
8
-
-
0038539610
-
The Mg2{thorn} binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations
-
Auffinger P, Bielecki L, Westhof E. 2003. The Mg2{thorn} binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations. Chem. Biol. 10: 551-561.
-
(2003)
Chem. Biol
, vol.10
, pp. 551-561
-
-
Auffinger, P.1
Bielecki, L.2
Westhof, E.3
-
9
-
-
34347404466
-
Nucleic acid solvation: Froms outside to insight
-
Auffinger P, Hashem Y. 2007. Nucleic acid solvation: froms outside to insight. Curr. Opin. Struct. Biol. 17: 325-333.
-
(2007)
Curr. Opin. Struct. Biol
, vol.17
, pp. 325-333
-
-
Auffinger, P.1
Hashem, Y.2
-
10
-
-
0034725528
-
Water and ion binding around RNA and DNA (C,G) oligomers
-
Auffinger P, Westhof E. 2000. Water and ion binding around RNA and DNA (C,G) oligomers. J. Mol. Biol. 300: 1113-1131.
-
(2000)
J. Mol. Biol
, vol.300
, pp. 1113-1131
-
-
Auffinger, P.1
Westhof, E.2
-
11
-
-
33745727284
-
Molecular dynamics simulations of DNA with polarizable force fields: Convergence of an ideal B-DNA structure to the crystallographic structure
-
Babin V, Baucom J, Darden TA, Sagui C. 2006. Molecular dynamics simulations of DNA with polarizable force fields: convergence of an ideal B-DNA structure to the crystallographic structure. J. Phys. Chem. B 110: 11571-11581.
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 11571-11581
-
-
Babin, V.1
Baucom, J.2
Darden, T.A.3
Sagui, C.4
-
12
-
-
0030623823
-
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
-
Bahar I, Atilgan A, Erman B. 1997. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des. 2: 173-181.
-
(1997)
Fold. Des
, vol.2
, pp. 173-181
-
-
Bahar, I.1
Atilgan, A.2
Erman, B.3
-
13
-
-
25844431698
-
Coarse-grained normal mode analysis in structural biology
-
Bahar I, Rader AJ. 2005. Coarse-grained normal mode analysis in structural biology. Curr. Opin. Struct. Biol. 15: 586-592.
-
(2005)
Curr. Opin. Struct. Biol
, vol.15
, pp. 586-592
-
-
Bahar, I.1
Rader, A.J.2
-
14
-
-
0037168282
-
Atomic radii for continuum electrostatics calculations on nucleic acids
-
Banavali NK, Roux B. 2002. Atomic radii for continuum electrostatics calculations on nucleic acids. J. Phys. Chem. B 106: 11026-11035.
-
(2002)
J. Phys. Chem. B
, vol.106
, pp. 11026-11035
-
-
Banavali, N.K.1
Roux, B.2
-
15
-
-
33646096731
-
Parametrization of a specific free energy function for automated docking against RNA targets using neural networks
-
Barbault F, Zhang LR, Zhang LH, Fan BT. 2006. Parametrization of a specific free energy function for automated docking against RNA targets using neural networks. Chemom. Intell. Lab. Syst. 82: 269-275.
-
(2006)
Chemom. Intell. Lab. Syst
, vol.82
, pp. 269-275
-
-
Barbault, F.1
Zhang, L.R.2
Zhang, L.H.3
Fan, B.T.4
-
16
-
-
33845700514
-
Riboswitches as antibacterial drug targets
-
Blount K, Breaker R. 2006. Riboswitches as antibacterial drug targets. Nat. Biotechnol. 24: 1558-1564.
-
(2006)
Nat. Biotechnol
, vol.24
, pp. 1558-1564
-
-
Blount, K.1
Breaker, R.2
-
17
-
-
49649112706
-
Multiscale modeling of nucleic acids: Insights into DNA flexibility
-
Bomble Y, Case D. 2008. Multiscale modeling of nucleic acids: insights into DNA flexibility. Biopolymers 89: 722-731.
-
(2008)
Biopolymers
, vol.89
, pp. 722-731
-
-
Bomble, Y.1
Case, D.2
-
18
-
-
0000991642
-
Harmonic dynamics of proteins: Normal modes and fluctuations in bovine pancreatic trypsin inhibitor
-
Brooks B, Karplus M. 1983. Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc. Natl Acad. Sci. U.S.A. 80: 6571-6575.
-
(1983)
Proc. Natl Acad. Sci. U.s.a
, vol.80
, pp. 6571-6575
-
-
Brooks, B.1
Karplus, M.2
-
19
-
-
33644535147
-
Natural products-the future scaffolds for novel antibiotics?
-
Butler MS, Buss AD. 2006. Natural products-the future scaffolds for novel antibiotics? Biochem. Pharmacol. 71: 919-929.
-
(2006)
Biochem. Pharmacol
, vol.71
, pp. 919-929
-
-
Butler, M.S.1
Buss, A.D.2
-
20
-
-
0042838304
-
Recognition of double-stranded RNA by proteins and small molecules
-
Carlson C, Stephens O, Beal P. 2003. Recognition of double-stranded RNA by proteins and small molecules. Biopolymers 70: 86-102.
-
(2003)
Biopolymers
, vol.70
, pp. 86-102
-
-
Carlson, C.1
Stephens, O.2
Beal, P.3
-
21
-
-
0034699519
-
Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics
-
Carter AP, Clemons WM, Brodersen DE, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V. 2000. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 407: 340-348.
-
(2000)
Nature
, vol.407
, pp. 340-348
-
-
Carter, A.P.1
Clemons, W.M.2
Brodersen, D.E.3
Morgan-Warren, R.J.4
Wimberly, B.T.5
Ramakrishnan, V.6
-
22
-
-
34249898353
-
Probing Na({thorn})-induced changes in the HIV-1 TAR conformational dynamics using NMR residual dipolar couplings: New insights into the role of counterions and electrostatic interactions in adaptive recognition
-
Casianonegroni A, Sun X, Al-Hashimi HM. 2007. Probing Na({thorn})-induced changes in the HIV-1 TAR conformational dynamics using NMR residual dipolar couplings: new insights into the role of counterions and electrostatic interactions in adaptive recognition. Biochemistry 46: 6525-6535.
-
(2007)
Biochemistry
, vol.46
, pp. 6525-6535
-
-
Casiano-Negroni, A.1
Sun, X.2
Al-Hashimi, H.M.3
-
23
-
-
1442351132
-
Protein flexibility in ligand docking and virtual screening to protein kinases
-
Cavasotto CN, Abagyan RA. 2004. Protein flexibility in ligand docking and virtual screening to protein kinases. J. Mol. Biol. 337: 209-225.
-
(2004)
J. Mol. Biol
, vol.337
, pp. 209-225
-
-
Cavasotto, C.N.1
Abagyan, R.A.2
-
24
-
-
21644473891
-
Representing receptor flexibility in ligand docking through relevant normal modes
-
Cavasotto CN, Kovacs JA, Abagyan RA. 2005. Representing receptor flexibility in ligand docking through relevant normal modes. J. Am. Chem. Soc. 127: 9632-9640.
-
(2005)
J. Am. Chem. Soc
, vol.127
, pp. 9632-9640
-
-
Cavasotto, C.N.1
Kovacs, J.A.2
Abagyan, R.A.3
-
25
-
-
2942547665
-
Simulation and modeling of nucleic acid structure, dynamics and interactions
-
Cheatham TE. 2004. Simulation and modeling of nucleic acid structure, dynamics and interactions. Curr. Opin. Struct. Biol. 14: 360-367.
-
(2004)
Curr. Opin. Struct. Biol
, vol.14
, pp. 360-367
-
-
Cheatham, T.E.1
-
26
-
-
0032922174
-
A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat
-
Cheatham TE, Cieplak P, Kollman PA. 1999. A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. J. Biomol. Struct. Dyn. 16: 845-862.
-
(1999)
J. Biomol. Struct. Dyn
, vol.16
, pp. 845-862
-
-
Cheatham, T.E.1
Cieplak, P.2
Kollman, P.A.3
-
27
-
-
0029170114
-
Molecular dynamics simulations on solvated biomolecular systems: The Particle Mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins
-
Cheatham TE, Miller JL, Fox T, Darden TA, Kollman PA. 1995. Molecular dynamics simulations on solvated biomolecular systems: the Particle Mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins. J. Amer. Chem. Soc. 117: 4193-4194.
-
(1995)
J. Amer. Chem. Soc
, vol.117
, pp. 4193-4194
-
-
Cheatham, T.E.1
Miller, J.L.2
Fox, T.3
Darden, T.A.4
Kollman, P.A.5
-
28
-
-
0030954877
-
Structure-based discovery of ligands targeted to the RNA double helix
-
Chen Q, Shafer RH, Kuntz ID. 1997. Structure-based discovery of ligands targeted to the RNA double helix. Biochemistry 36: 11402-11407.
-
(1997)
Biochemistry
, vol.36
, pp. 11402-11407
-
-
Chen, Q.1
Shafer, R.H.2
Kuntz, I.D.3
-
29
-
-
84986516411
-
Application of the multimolecule and multiconformational RESP methodology to bio-polymers -charge derivation for DNA, RNA and proteins
-
Cieplak P, Cornell WD, Bayly C, Kollman PA. 1995. Application of the multimolecule and multiconformational RESP methodology to bio-polymers -charge derivation for DNA, RNA and proteins. J. Comput. Chem. 16: 1357-1377.
-
(1995)
J. Comput. Chem
, vol.16
, pp. 1357-1377
-
-
Cieplak, P.1
Cornell, W.D.2
Bayly, C.3
Kollman, P.A.4
-
30
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM Jr, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117: 5179-5197.
-
(1995)
J. Am. Chem. Soc
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz Jr., K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
31
-
-
0042337396
-
Sequence and structure space of RNA-binding peptides
-
Das C, Frankel A. 2003. Sequence and structure space of RNA-binding peptides. Biopolymers 70: 80-85.
-
(2003)
Biopolymers
, vol.70
, pp. 80-85
-
-
Das, C.1
Frankel, A.2
-
32
-
-
3843057001
-
Validation of automated docking programs for docking and database screening against RNA drug targets
-
Detering C, Varani G. 2004. Validation of automated docking programs for docking and database screening against RNA drug targets. J. Med. Chem. 47: 4188-4201.
-
(2004)
J. Med. Chem
, vol.47
, pp. 4188-4201
-
-
Detering, C.1
Varani, G.2
-
33
-
-
1242274330
-
A guide to ions and RNA structure
-
Draper DE. 2004. A guide to ions and RNA structure. RNA 3: 335-343.
-
(2004)
Rna
, vol.3
, pp. 335-343
-
-
Draper, D.E.1
-
34
-
-
0028454915
-
New approach for determining low-frequency normal-modes in macromolecules
-
Durand P, Trinquier G, Sanejouand YH. 1994. New approach for determining low-frequency normal-modes in macromolecules. Biopolymers 34: 759-771.
-
(1994)
Biopolymers
, vol.34
, pp. 759-771
-
-
Durand, P.1
Trinquier, G.2
Sanejouand, Y.H.3
-
35
-
-
33750407288
-
Anisotropic network model: Systematic evaluation and a new web interface
-
Eyal E, Yang L-W, Bahar I. 2006. Anisotropic network model: systematic evaluation and a new web interface. Bioinformatics 22: 2619-2627.
-
(2006)
Bioinformatics
, vol.22
, pp. 2619-2627
-
-
Eyal, E.1
Yang, L.-W.2
Bahar, I.3
-
36
-
-
41849090144
-
NMR and MD studies of the temperature-dependent dynamics of RNA YNMG-tetraloops
-
Ferner J, Villa A, Duchardt E, Widjajakusuma E, Wohnert J, Stock G, Schwalbe H. 2008. NMR and MD studies of the temperature-dependent dynamics of RNA YNMG-tetraloops. Nucleic Acid. Res. 36: 1928-1940.
-
(2008)
Nucleic Acid. Res
, vol.36
, pp. 1928-1940
-
-
Ferner, J.1
Villa, A.2
Duchardt, E.3
Widjajakusuma, E.4
Wohnert, J.5
Stock, G.6
Schwalbe, H.7
-
37
-
-
0033949057
-
Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR
-
Filikov AV, Mohan V, Vickers TA, Griffey RH, Cook PD, Abagyan RA, James TL. 2000. Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR. J. Comput. Aid. Mol. Des. 14: 593-610.
-
(2000)
J. Comput. Aid. Mol. Des
, vol.14
, pp. 593-610
-
-
Filikov, A.V.1
Mohan, V.2
Vickers, T.A.3
Griffey, R.H.4
Cook, P.D.5
Abagyan, R.A.6
James, T.L.7
-
38
-
-
1342343126
-
A structure-based strategy to identify new molecular scaffolds target-ing the bacterial ribosomal A-site
-
Foloppe N, Chen IJ, Davis B, Hold A, Morley D, Howes R. 2004. A structure-based strategy to identify new molecular scaffolds target-ing the bacterial ribosomal A-site. Bioorg. Med. Chem. 12: 935-947.
-
(2004)
Bioorg. Med. Chem
, vol.12
, pp. 935-947
-
-
Foloppe, N.1
Chen, I.J.2
Davis, B.3
Hold, A.4
Morley, D.5
Howes, R.6
-
39
-
-
0348244547
-
All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and con-densed phase macromolecular target data
-
Foloppe N, MacKerell AD. 2000. All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and con-densed phase macromolecular target data. J. Comput. Chem. 21: 86-104.
-
(2000)
J. Comput. Chem
, vol.21
, pp. 86-104
-
-
Foloppe, N.1
Mackerell, A.D.2
-
40
-
-
33750274718
-
Towards the discovery of drug-like RNA ligands? Drug Disc
-
Foloppe N, Matassova N, Aboul-Ela F. 2006. Towards the discovery of drug-like RNA ligands? Drug Disc. Today 11: 1019-1027.
-
(2006)
Today
, vol.11
, pp. 1019-1027
-
-
Foloppe, N.1
Matassova, N.2
Aboul-Ela, F.3
-
41
-
-
0032571359
-
Paromomycin binding induces a local conformational change in the A-site of 16 S rRNA
-
Fourmy D, Yoshizawa S, Puglisi JD. 1998. Paromomycin binding induces a local conformational change in the A-site of 16 S rRNA. J. Mol. Biol. 277: 333-345.
-
(1998)
J. Mol. Biol
, vol.277
, pp. 333-345
-
-
Fourmy, D.1
Yoshizawa, S.2
Puglisi, J.D.3
-
43
-
-
44849090619
-
Analysing the flexibility of RNA structures by constraint counting
-
Fulle S, Gohlke H. 2008. Analysing the flexibility of RNA structures by constraint counting. Biophys. J. 94: 4202-4219.
-
(2008)
Biophys. J
, vol.94
, pp. 4202-4219
-
-
Fulle, S.1
Gohlke, H.2
-
44
-
-
61649098586
-
Statics of the ribosomal exit tunnel: Implications for co-translational peptide folding, elongation regulation, and anti-biotics binding
-
Fulle S, Gohlke H. 2009a. Statics of the ribosomal exit tunnel: implications for co-translational peptide folding, elongation regulation, and anti-biotics binding. J. Mol. Biol. 387: 502-517.
-
(2009)
J. Mol. Biol
, vol.387
, pp. 502-517
-
-
Fulle, S.1
Gohlke, H.2
-
45
-
-
70349299861
-
Constraint counting on RNA structures: Linking flexibility and function
-
Fulle S, Gohlke H. 2009b. Constraint counting on RNA structures: linking flexibility and function. Methods 49: 181-188.
-
(2009)
Methods
, vol.49
, pp. 181-188
-
-
Fulle, S.1
Gohlke, H.2
-
46
-
-
0034783659
-
Targeting RNA with small-molecule drugs: Therapeutic promise and chemical challenges
-
Gallego J, Varani G. 2001. Targeting RNA with small-molecule drugs: therapeutic promise and chemical challenges. Acc. Chem. Res. 34: 836-843.
-
(2001)
Acc. Chem. Res
, vol.34
, pp. 836-843
-
-
Gallego, J.1
Varani, G.2
-
47
-
-
0033135209
-
Theoretical calculations, synthesis and base pairing properties of oligonucleo-tides containing 8-amino-2'-deoxyadenosine
-
Garcia RG, Ferrer E, Macias MJ, Eritja R, Orozco M. 1999. Theoretical calculations, synthesis and base pairing properties of oligonucleo-tides containing 8-amino-2'-deoxyadenosine. Nucleic Acids Res. 27: 1991-1998.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 1991-1998
-
-
Garcia, R.G.1
Ferrer, E.2
Macias, M.J.3
Eritja, R.4
Orozco, M.5
-
48
-
-
34547820982
-
NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings
-
Getz M, Sun X, Casiano-Negroni A, Zhang Q, Al-Hashimi HM. 2007. NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings. Biopolymers 86: 384-402.
-
(2007)
Biopolymers
, vol.86
, pp. 384-402
-
-
Getz, M.1
Sun, X.2
-
49
-
-
0036286321
-
Simulations of nucleic acids and their com-plexes
-
Giudice E, Lavery R. 2002. Simulations of nucleic acids and their com-plexes. Acc. Chem. Res. 35: 350-357.
-
(2002)
Acc. Chem. Res
, vol.35
, pp. 350-357
-
-
Giudice, E.1
Lavery, R.2
-
50
-
-
0020771265
-
Dynamics of a small globular protein in terms of low-frequency vibrational modes
-
Go N, Noguti T, Nishikawa T. 1983. Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc. Natl Acad. Sci. U.S.A. 80: 3696-3700.
-
(1983)
Proc. Natl Acad. Sci. U.s.a
, vol.80
, pp. 3696-3700
-
-
Go, N.1
Noguti, T.2
Nishikawa, T.3
-
51
-
-
0034645763
-
Knowledge-based scoring function to predict protein-ligand interactions
-
Gohlke H, Hendlich M, Klebe G. 2000. Knowledge-based scoring function to predict protein-ligand interactions. J. Mol. Biol. 295: 337-356.
-
(2000)
J. Mol. Biol
, vol.295
, pp. 337-356
-
-
Gohlke, H.1
Hendlich, M.2
Klebe, G.3
-
52
-
-
0037008160
-
Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors
-
Gohlke H, Klebe G. 2002. Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors. Angew. Chem. Int. Ed. 41: 2645-2676.
-
(2002)
Angew. Chem. Int. Ed
, vol.41
, pp. 2645-2676
-
-
Gohlke, H.1
Klebe, G.2
-
53
-
-
0043245780
-
Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes
-
Gohlke H, Kiel C, Case DA. 2003. Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. J. Mol. Biol. 330: 891-913.
-
(2003)
J. Mol. Biol
, vol.330
, pp. 891-913
-
-
Gohlke, H.1
Kiel, C.2
Case, D.A.3
-
54
-
-
33748448490
-
A natural coarse graining for simulating large biomolecular motion
-
Gohlke H, Thorpe MF. 2006. A natural coarse graining for simulating large biomolecular motion. Biophys. J. 91: 2115-2120.
-
(2006)
Biophys. J
, vol.91
, pp. 2115-2120
-
-
Gohlke, H.1
Thorpe, M.F.2
-
55
-
-
0037234043
-
Free energy calculations for theophylline binding to an RNA aptamer: MM-PBSA and comparison of thermodynamic integration methods
-
Gouda H, Kuntz ID, Case DA, Kollman PA. 2003. Free energy calculations for theophylline binding to an RNA aptamer: MM-PBSA and comparison of thermodynamic integration methods. Biopolymers 68: 16-34.
-
(2003)
Biopolymers
, vol.68
, pp. 16-34
-
-
Gouda, H.1
Kuntz, I.D.2
Case, D.A.3
Kollman, P.A.4
-
56
-
-
47349127321
-
Docking to RNA via root-mean-square-deviation-driven energy minimization with flexible ligands and flexible targets
-
Guilbert C, James T. 2008. Docking to RNA via root-mean-square-deviation-driven energy minimization with flexible ligands and flexible targets. J. Chem. Inf. Mod. 48: 1257-1268.
-
(2008)
J. Chem. Inf. Mod
, vol.48
, pp. 1257-1268
-
-
Guilbert, C.1
James, T.2
-
57
-
-
0037012422
-
Design of novel antibiotics that bind to the ribosomal acyltransfer site
-
Haddad J, Kotra LP, Llano-Sotelo B, Kim C, Azucena EF, Liu M, Vakulenko SB, Chow CS, Mobashery S. 2002. Design of novel antibiotics that bind to the ribosomal acyltransfer site. J. Am. Chem. Soc. 124: 3229-3237.
-
(2002)
J. Am. Chem. Soc
, vol.124
, pp. 3229-3237
-
-
Haddad, J.1
Kotra, L.P.2
Llano-Sotelo, B.3
Kim, C.4
Azucena, E.F.5
Liu, M.6
Vakulenko, S.B.7
Chow, C.S.8
Mobashery, S.9
-
58
-
-
0036342198
-
The structures of four macrolide antibiotics bound to the large ribosomal subunit
-
Hansen J, Ippolito J, Ban N, Nissen P, Moore P, Steitz T. 2002. The structures of four macrolide antibiotics bound to the large ribosomal subunit. Mol. Cell 10: 117-128.
-
(2002)
Mol. Cell
, vol.10
, pp. 117-128
-
-
Hansen, J.1
Ippolito, J.2
Ban, N.3
Nissen, P.4
Moore, P.5
Steitz, T.6
-
59
-
-
59649095963
-
A short guide for molecular dynamics simulations of RNA systems
-
Hashem Y, Auffinger P. 2009. A short guide for molecular dynamics simulations of RNA systems. Methods 47: 187-197.
-
(2009)
Methods
, vol.47
, pp. 187-197
-
-
Hashem, Y.1
Auffinger, P.2
-
60
-
-
0036761206
-
Rational ligand design for RNA: The role of static structure and conformational flexibility in target recognition
-
Hermann T. 2002. Rational ligand design for RNA: the role of static structure and conformational flexibility in target recognition. Biochimie 84: 869-875.
-
(2002)
Biochimie
, vol.84
, pp. 869-875
-
-
Hermann, T.1
-
61
-
-
0041836268
-
Chemical and functional diversity of small molecule ligands for RNA
-
Hermann T. 2003. Chemical and functional diversity of small molecule ligands for RNA. Biopolymers 70: 4-18.
-
(2003)
Biopolymers
, vol.70
, pp. 4-18
-
-
Hermann, T.1
-
62
-
-
0031933080
-
RNA as a drug target: Chemical, modelling, and evolutionary tools
-
Hermann T, Westhof E. 1998. RNA as a drug target: chemical, modelling, and evolutionary tools. Curr. Opin. Biotechnol. 9: 66-73.
-
(1998)
Curr. Opin. Biotechnol
, vol.9
, pp. 66-73
-
-
Hermann, T.1
Westhof, E.2
-
63
-
-
0033535566
-
Docking of cationic antibiotics to negatively charged pockets in RNA folds
-
Hermann T, Westhof E. 1999. Docking of cationic antibiotics to negatively charged pockets in RNA folds. J. Med. Chem. 42: 1250-1261.
-
(1999)
J. Med. Chem
, vol.42
, pp. 1250-1261
-
-
Hermann, T.1
Westhof, E.2
-
64
-
-
9144263145
-
Structural rigidity in the capsid assembly of cowpea chlorotic mottle virus
-
Hespenheide BM, Jacobs DJ, Thorpe MF. 2004. Structural rigidity in the capsid assembly of cowpea chlorotic mottle virus. J. Phys.: Condens. Matter 16: 5055-5064.
-
(2004)
J. Phys.: Condens. Matter
, vol.16
, pp. 5055-5064
-
-
Hespenheide, B.M.1
Jacobs, D.J.2
Thorpe, M.F.3
-
65
-
-
33846000313
-
Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking
-
Huang SY, Zou XQ. 2007. Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking. Proteins 66: 399-421.
-
(2007)
Proteins
, vol.66
, pp. 399-421
-
-
Huang, S.Y.1
Zou, X.Q.2
-
66
-
-
45749089015
-
Crystal structure of the oxazolidinone antibiotic linezolid bound to the 50S ribosomal subunit
-
Ippolito JA, Kanyo ZF, Wang D, Franceschi FJ, Moore PB, Steitz TA, Duffy EM. 2008. Crystal structure of the oxazolidinone antibiotic linezolid bound to the 50S ribosomal subunit. J. Med. Chem. 51: 3353-3356.
-
(2008)
J. Med. Chem
, vol.51
, pp. 3353-3356
-
-
Ippolito, J.A.1
Kanyo, Z.F.2
Wang, D.3
Franceschi, F.J.4
Moore, P.B.5
Steitz, T.A.6
Duffy, E.M.7
-
67
-
-
0032543957
-
A 1.3-A resolution crystal structure of the HIV-1 trans-activation response region RNA stem reveals a metal ion-dependent bulge conformation
-
Ippolito JA, Steitz TA. 1998. A 1.3-A resolution crystal structure of the HIV-1 trans-activation response region RNA stem reveals a metal ion-dependent bulge conformation. Proc. Natl Acad. Sci. U.S.A. 95: 9819-9824.
-
(1998)
Proc. Natl Acad. Sci. U.s.a
, vol.95
, pp. 9819-9824
-
-
Ippolito, J.A.1
Steitz, T.A.2
-
68
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen W, Chandrasekhar J, Madura J, Impey R, Klein M. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79: 926-935.
-
(1983)
J. Chem. Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.1
Chandrasekhar, J.2
Madura, J.3
Impey, R.4
Klein, M.5
-
69
-
-
1242272760
-
Calculation of ligand-nucleic acid binding free energies with the generalized-born model in DOCK
-
Kang XS, Shafer RH, Kuntz ID. 2004. Calculation of ligand-nucleic acid binding free energies with the generalized-born model in DOCK. Biopolymers 73: 192-204.
-
(2004)
Biopolymers
, vol.73
, pp. 192-204
-
-
Kang, X.S.1
Shafer, R.H.2
Kuntz, I.D.3
-
70
-
-
68149149959
-
Elastic potential grids: Accurate and efficient representation of intermolecular interactions for fully flexible docking
-
Kazemi S, Kruger DM, Sirockin F, Gohlke H. 2009. Elastic potential grids: accurate and efficient representation of intermolecular interactions for fully flexible docking. ChemMedChem 4: 1264-1268.
-
(2009)
Chemmedchem
, vol.4
, pp. 1264-1268
-
-
Kazemi, S.1
Kruger, D.M.2
Sirockin, F.3
Gohlke, H.4
-
71
-
-
0032540504
-
NMR structure of a classical pseudoknot: Interplay of single-and double-stranded RNA
-
Kolk MH, van der Graaf M, Wijmenga SS, Pleij CW, Heus HA, Hilbers CW. 1998. NMR structure of a classical pseudoknot: interplay of single-and double-stranded RNA. Science 280: 434-438.
-
(1998)
Science
, vol.280
, pp. 434-438
-
-
Kolk, M.H.1
van der Graaf, M.2
Wijmenga, S.S.3
Pleij, C.W.4
Heus, H.A.5
Hilbers, C.W.6
-
72
-
-
59449095246
-
Determinants of the unexpected stability of RNA fluorobenzene self pairs
-
Kopitz H, Zivkovic A, Engels JW, Gohlke H. 2008. Determinants of the unexpected stability of RNA fluorobenzene self pairs. ChemBioChem 9: 2619-2622.
-
(2008)
Chembiochem
, vol.9
, pp. 2619-2622
-
-
Kopitz, H.1
Zivkovic, A.2
Engels, J.W.3
Gohlke, H.4
-
73
-
-
84961979116
-
Affinity and specificity of protein U1A-RNA complex formation based on an additive component free energy model
-
Kormos BL, Benitex Y, Baranger AM, Beveridge DL. 2007. Affinity and specificity of protein U1A-RNA complex formation based on an additive component free energy model. J. Mol. Biol. 371: 1405-1419.
-
(2007)
J. Mol. Biol
, vol.371
, pp. 1405-1419
-
-
Kormos, B.L.1
Benitex, Y.2
Baranger, A.M.3
Beveridge, D.L.4
-
74
-
-
66149167201
-
Collective dynamics of the ribosomal tunnel revealed by elastic network modeling
-
Kurkcuoglu O, Kurkcuoglu Z, Doruker P, Jernigan RL. 2008. Collective dynamics of the ribosomal tunnel revealed by elastic network modeling. Proteins 75: 837-845.
-
(2008)
Proteins
, vol.75
, pp. 837-845
-
-
Kurkcuoglu, O.1
Kurkcuoglu, Z.2
Doruker, P.3
Jernigan, R.L.4
-
75
-
-
66449110287
-
DOC 6: Combining techniques to model RNA-small molecul complexes
-
Lang PT, Brozell SR, Mukherjee S, Pettersen EF, Meng EC, Thomas V, Rizzo RC, Case DA, James TL, Kuntz ID. 2009. DOC 6: combining techniques to model RNA-small molecul complexes. RNA 15: 1219-1230.
-
(2009)
Rna
, vol.15
, pp. 1219-1230
-
-
Lang, P.T.1
Brozell, S.R.2
Mukherjee, S.3
Pettersen, E.F.4
Meng, E.C.5
Thomas, V.6
Rizzo, R.C.7
Case, D.A.8
James, T.L.9
Kuntz, I.D.10
-
76
-
-
0031894779
-
Modeling RNA-ligand interactions: The Rev-binding element RNA-aminoglycoside complex
-
Leclerc F, Cedergren R. 1998. Modeling RNA-ligand interactions: the Rev-binding element RNA-aminoglycoside complex. J. Med. Chem. 41: 175-182.
-
(1998)
J. Med. Chem
, vol.41
, pp. 175-182
-
-
Leclerc, F.1
Cedergren, R.2
-
77
-
-
0033443536
-
MCSS-based predictions of RNA binding sites
-
Leclerc F, Karplus M. 1999. MCSS-based predictions of RNA binding sites. Theor. Chem. Acc. 101: 131-137.
-
(1999)
Theor. Chem. Acc
, vol.101
, pp. 131-137
-
-
Leclerc, F.1
Karplus, M.2
-
78
-
-
0035838382
-
Current topics in RNA-protein recognition: Control of specificity and biological function through induced fit and conformational capture
-
Leulliot N, Varani G. 2001. Current topics in RNA-protein recognition: control of specificity and biological function through induced fit and conformational capture. Biochemistry 40: 7947-7956.
-
(2001)
Biochemistry
, vol.40
, pp. 7947-7956
-
-
Leulliot, N.1
Varani, G.2
-
79
-
-
0036840202
-
A coarse-grained normal mode approach for macro-molecules: An efficient implementation and application to Ca2{thorn}-ATPase
-
Li GH, Cui Q. 2002. A coarse-grained normal mode approach for macro-molecules: an efficient implementation and application to Ca2{thorn}-ATPase. Biophys. J. 83: 2457-2474.
-
(2002)
Biophys. J
, vol.83
, pp. 2457-2474
-
-
Li, G.H.1
Cui, Q.2
-
80
-
-
0036008846
-
Structure-based computational database screening, in vitro assay, and NMR assess-ment of compounds that target TAR RNA
-
Lind KE, Du Z, Fujinaga K, Peterlin BM, James TL. 2002. Structure-based computational database screening, in vitro assay, and NMR assess-ment of compounds that target TAR RNA. Chem. Biol. 9: 185-193.
-
(2002)
Chem. Biol
, vol.9
, pp. 185-193
-
-
Lind, K.E.1
Du, Z.2
Fujinaga, K.3
Peterlin, B.M.4
James, T.L.5
-
81
-
-
0032533772
-
RNA bulge entropies in the unbound state correlate with peptide binding strengths for HIV-1 and BIV TAR RNA because of improved conformational access
-
Lustig B, Bahar I, Jernigan RL. 1998. RNA bulge entropies in the unbound state correlate with peptide binding strengths for HIV-1 and BIV TAR RNA because of improved conformational access. Nucleic Acids Res. 26: 5212-5217.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 5212-5217
-
-
Lustig, B.1
Bahar, I.2
Jernigan, R.L.3
-
82
-
-
0037138652
-
Binding of aminoglycoside antibiotics to the small ribosomal subunit: A continuum electrostatics investigation
-
Ma C, Baker N, Joseph S, McCammon J. 2002. Binding of aminoglycoside antibiotics to the small ribosomal subunit: a continuum electrostatics investigation. J. Am. Chem. Soc. 124: 1438-1442.
-
(2002)
J. Am. Chem. Soc
, vol.124
, pp. 1438-1442
-
-
Ma, C.1
Baker, N.2
Joseph, S.3
McCammon, J.4
-
83
-
-
3142714765
-
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distri-butions in molecular dynamics simulations
-
Mackerell AD, Feig M, Brooks CL. 2004. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distri-butions in molecular dynamics simulations. J. Comput. Chem. 25: 1400-1415.
-
(2004)
J. Comput. Chem
, vol.25
, pp. 1400-1415
-
-
Mackerell, A.D.1
Feig, M.2
Brooks, C.L.3
-
84
-
-
41949124146
-
Molecular dynamics simulations of nucleic acid-protein complexes
-
MacKerell AD, Nilsson L. 2008. Molecular dynamics simulations of nucleic acid-protein complexes. Curr. Opin. Struct. Biol. 18: 194-199.
-
(2008)
Curr. Opin. Struct. Biol
, vol.18
, pp. 194-199
-
-
Mackerell, A.D.1
Nilsson, L.2
-
85
-
-
33847318371
-
Molecular dynamics simulations of RNA: An in silico single molecule approach
-
McDowell ES, Spackoá Na, Sponer J, Walter N. 2007. Molecular dynamics simulations of RNA: an in silico single molecule approach. Biopolymers 85: 169-184.
-
(2007)
Biopolymers
, vol.85
, pp. 169-184
-
-
McDowell, E.S.1
Spackoá, N.2
Sponer, J.3
Walter, N.4
-
86
-
-
34249277111
-
Conformational transition in the aminoacyl t-RNA site of the bacterial ribosome both in the presence and absence of an aminoglycoside antibiotic
-
Meroueh SO, Mobashery S. 2007. Conformational transition in the aminoacyl t-RNA site of the bacterial ribosome both in the presence and absence of an aminoglycoside antibiotic. Chem. Biol. Drug Des. 69: 291-297.
-
(2007)
Chem. Biol. Drug Des
, vol.69
, pp. 291-297
-
-
Meroueh, S.O.1
Mobashery, S.2
-
87
-
-
17144441957
-
On secondary structure rearrangements and equilibria of small RNAs
-
Micura R, Hobartner C. 2003. On secondary structure rearrangements and equilibria of small RNAs. ChemBioChem 4: 984-990.
-
(2003)
Chembiochem
, vol.4
, pp. 984-990
-
-
Micura, R.1
Hobartner, C.2
-
88
-
-
0036295964
-
The linkage between magnesium binding and RNA folding
-
Misra VK, Draper DE. 2002. The linkage between magnesium binding and RNA folding. J. Mol. Biol. 317: 507-521.
-
(2002)
J. Mol. Biol
, vol.317
, pp. 507-521
-
-
Misra, V.K.1
Draper, D.E.2
-
89
-
-
32344449937
-
Docking of aminoglycosides to hydrated and flexible RNA
-
Moitessier N, Westhof E, Hanessian S. 2006. Docking of aminoglycosides to hydrated and flexible RNA. J. Med. Chem. 49: 1023-1033.
-
(2006)
J. Med. Chem
, vol.49
, pp. 1023-1033
-
-
Moitessier, N.1
Westhof, E.2
Hanessian, S.3
-
90
-
-
4043058000
-
Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock
-
Morley SD, Afshar M. 2004. Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock. J. Comput. Aid. Mol. Des. 18: 189-208.
-
(2004)
J. Comput. Aid. Mol. Des
, vol.18
, pp. 189-208
-
-
Morley, S.D.1
Afshar, M.2
-
91
-
-
33646169319
-
Conformational dynamics of RNA-peptide binding: A molecular dynamics simulation study
-
Mu Y, Stock G. 2006. Conformational dynamics of RNA-peptide binding: a molecular dynamics simulation study. Biophys. J. 90: 391-399.
-
(2006)
Biophys. J
, vol.90
, pp. 391-399
-
-
Mu, Y.1
Stock, G.2
-
92
-
-
32844459761
-
Interactions of designer antibiotics and the bacterial ribosomal aminoacyl-tRNA site
-
Murray J, Meroueh S, Russell R, Lentzen G, Haddad J, Mobashery S. 2006. Interactions of designer antibiotics and the bacterial ribosomal aminoacyl-tRNA site. Chem. Biol. 13: 129-138.
-
(2006)
Chem. Biol
, vol.13
, pp. 129-138
-
-
Murray, J.1
Meroueh, S.2
Russell, R.3
Lentzen, G.4
Haddad, J.5
Mobashery, S.6
-
93
-
-
37349085453
-
A flexible approach to induced fit docking
-
Nabuurs SB, Wagener M, De Vlieg J. 2007. A flexible approach to induced fit docking. J. Med. Chem. 50: 6507-6518.
-
(2007)
J. Med. Chem
, vol.50
, pp. 6507-6518
-
-
Nabuurs, S.B.1
Wagener, M.2
de Vlieg, J.3
-
94
-
-
0034671676
-
Molecular dynamics studies of the HIV-1 TAR and its complex with argininamide
-
Nifosi R, Reyes CM, Kollman PA. 2000. Molecular dynamics studies of the HIV-1 TAR and its complex with argininamide. Nucleic Acids Res. 28: 4944-4955.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 4944-4955
-
-
Nifosi, R.1
Reyes, C.M.2
Kollman, P.A.3
-
95
-
-
0035805229
-
Recognition of cognate transfer RNA by the 30S ribosomal subunit
-
Ogle JM, Brodersen DE, Clemons WM, Tarry MJ, Carter AP, Ramakrishnan V. 2001. Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292: 897-902.
-
(2001)
Science
, vol.292
, pp. 897-902
-
-
Ogle, J.M.1
Brodersen, D.E.2
Clemons, W.M.3
Tarry, M.J.4
Carter, A.P.5
Ramakrishnan, V.6
-
96
-
-
0034314630
-
Theoretical methods for the description of the solvent effect in biomolecular systems
-
Orozco M, Luque FJ., 2000. Theoretical methods for the description of the solvent effect in biomolecular systems. Chem. Rev. 100: 4187-4225.
-
(2000)
Chem. Rev
, vol.100
, pp. 4187-4225
-
-
Orozco, M.1
Luque, F.J.2
-
97
-
-
42149084972
-
Recent advances in the study of nucleic acid flexibility by molecular dynamics
-
Orozco M, Noy A, Perez A. 2008. Recent advances in the study of nucleic acid flexibility by molecular dynamics. Curr. Opin. Struct. Biol. 18: 185-193.
-
(2008)
Curr. Opin. Struct. Biol
, vol.18
, pp. 185-193
-
-
Orozco, M.1
Noy, A.2
Perez, A.3
-
98
-
-
1242347628
-
Theoretical methods for the simulation of nucleic acids
-
Orozco M, Perez A, Noy A, Luque FJ., 2003. Theoretical methods for the simulation of nucleic acids. Chem. Soc. Rev. 32: 350-364.
-
(2003)
Chem. Soc. Rev
, vol.32
, pp. 350-364
-
-
Orozco, M.1
Perez, A.2
Noy, A.3
Luque, F.J.4
-
99
-
-
36749098380
-
Dynamics of B-DNA on the micro-second time scale
-
Perez A, Luque FJ, Orozco M. 2007a. Dynamics of B-DNA on the micro-second time scale. J. Am. Chem. Soc. 129: 14739-14745.
-
(2007)
J. Am. Chem. Soc
, vol.129
, pp. 14739-14745
-
-
Perez, A.1
Luque, F.J.2
Orozco, M.3
-
100
-
-
34250318638
-
Refinement of the AMBER force field for nucleic acids: Improving the description of a/g conformers
-
Perez A, Marchan I, Svozil D, Sponer J, Cheatham T, Laughton C, Orozco M. 2007b. Refinement of the AMBER force field for nucleic acids: improving the description of a/g conformers. Biophys. J. 92: 3817-3829.
-
(2007)
Biophys. J
, vol.92
, pp. 3817-3829
-
-
Perez, A.1
Marchan, I.2
Svozil, D.3
Sponer, J.4
Cheatham, T.5
Laughton, C.6
Orozco, M.7
-
101
-
-
35248883964
-
DrugScoreRNA -knowledge-based scoring function to predict RNA-ligand interactions
-
Pfeffer P, Gohlke H. 2007. DrugScoreRNA -knowledge-based scoring function to predict RNA-ligand interactions. J. Chem. Inf. Mod. 47: 1868-1876.
-
(2007)
J. Chem. Inf. Mod
, vol.47
, pp. 1868-1876
-
-
Pfeffer, P.1
Gohlke, H.2
-
102
-
-
0242443693
-
Force fields for protein simulations: Adv
-
Ponder JW, Case DA. 2003. Force fields for protein simulations: Adv. Protein Chem. 66: 27-85.
-
(2003)
Protein Chem
, vol.66
, pp. 27-85
-
-
Ponder, J.W.1
Case, D.A.2
-
103
-
-
0026651395
-
Conformation of the TAR RNA-arginine complex by NMR spectroscopy
-
Puglisi JD, Tan R, Calnan BJ, Frankel AD, Williamson JR. 1992. Conformation of the TAR RNA-arginine complex by NMR spectroscopy. Science 257: 76-80.
-
(1992)
Science
, vol.257
, pp. 76-80
-
-
Puglisi, J.D.1
Tan, R.2
Calnan, B.J.3
Frankel, A.D.4
Williamson, J.R.5
-
104
-
-
34250629636
-
Chemical parameters influencing fine-tuning in the binding of macrolide antibiotics to the ribosomal tunnel
-
Pyetan E, Baram D, Auerbach-Nevo T, Yonath A. 2007. Chemical parameters influencing fine-tuning in the binding of macrolide antibiotics to the ribosomal tunnel. Pure Appl. Chem. 79: 955-968.
-
(2007)
Pure Appl. Chem
, vol.79
, pp. 955-968
-
-
Pyetan, E.1
Baram, D.2
Auerbach-Nevo, T.3
Yonath, A.4
-
105
-
-
33746388359
-
Structure, dynamics, and elasticity of free 16S rRNA helix 44 studied by molecular dynamics simulations
-
Réblová K, Lankaš F, Rázga F, Krasovska MV, Koča J, Šponer J. 2006. Structure, dynamics, and elasticity of free 16S rRNA helix 44 studied by molecular dynamics simulations. Biopolymers 82: 504-520.
-
(2006)
Biopolymers
, vol.82
, pp. 504-520
-
-
Réblová, K.1
Lankaš, F.2
Rázga, F.3
Krasovska, M.V.4
Koča, J.5
Šponer, J.6
-
106
-
-
0034646574
-
Structure and thermodynamics of RNA-protein binding: Using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change
-
Reyes CM, Kollman PA. 2000a. Structure and thermodynamics of RNA-protein binding: using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change. J. Mol. Biol. 297: 1145-1158.
-
(2000)
J. Mol. Biol
, vol.297
, pp. 1145-1158
-
-
Reyes, C.M.1
Kollman, P.A.2
-
107
-
-
0034614387
-
Investigating the binding specificity of U1A-RNA by computational mutagenesis
-
Reyes CM, Kollman PA. 2000b. Investigating the binding specificity of U1A-RNA by computational mutagenesis. J. Mol. Biol. 295: 1-6.
-
(2000)
J. Mol. Biol
, vol.295
, pp. 1-6
-
-
Reyes, C.M.1
Kollman, P.A.2
-
108
-
-
0034999080
-
Molecular dynamics and binding specificity analysis of the bovine immunodeficiency virus BIV Tat-TAR complex
-
Reyes CM, Nifosi R, Frankel AD, Kollman PA. 2001. Molecular dynamics and binding specificity analysis of the bovine immunodeficiency virus BIV Tat-TAR complex. Biophys. J. 80: 2833-2842.
-
(2001)
Biophys. J
, vol.80
, pp. 2833-2842
-
-
Reyes, C.M.1
Nifosi, R.2
Frankel, A.D.3
Kollman, P.A.4
-
109
-
-
33750899801
-
Estimation of absolute free energies of hydration using continuum methods: Accuracy of partial, charge models and optimization of nonpolar contributions
-
Rizzo RC, Aynechi T, Case DA, Kuntz ID. 2006. Estimation of absolute free energies of hydration using continuum methods: accuracy of partial, charge models and optimization of nonpolar contributions. J. Chem. Theor. Comput. 2: 128-139.
-
(2006)
J. Chem. Theor. Comput
, vol.2
, pp. 128-139
-
-
Rizzo, R.C.1
Aynechi, T.2
Case, D.A.3
Kuntz, I.D.4
-
110
-
-
0037467430
-
The complex of a designer antibiotic with a model aminoacyl site of the 30S ribosomal subunit revealed by X-ray crystallography
-
Russell RJ, Murray JB, Lentzen G, Haddad J, Mobashery S. 2003. The complex of a designer antibiotic with a model aminoacyl site of the 30S ribosomal subunit revealed by X-ray crystallography. J. Am. Chem. Soc. 125: 3410-3411.
-
(2003)
J. Am. Chem. Soc
, vol.125
, pp. 3410-3411
-
-
Russell, R.J.1
Murray, J.B.2
Lentzen, G.3
Haddad, J.4
Mobashery, S.5
-
111
-
-
0034268836
-
Structure of functionally activated small ribosomal subunit at 3.3 angstrom resolution
-
Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, Janell D, Bashan A, Bartels H, Agmon I, Franceschi F, Yonath A. 2000. Structure of functionally activated small ribosomal subunit at 3.3 angstrom resolution. Cell 102: 615-623.
-
(2000)
Cell
, vol.102
, pp. 615-623
-
-
Schluenzen, F.1
Tocilj, A.2
Zarivach, R.3
Harms, J.4
Gluehmann, M.5
Janell, D.6
Bashan, A.7
Bartels, H.8
Agmon, I.9
Franceschi, F.10
Yonath, A.11
-
112
-
-
0037334850
-
Structural basis for the antibiotic activity of ketolides and azalides
-
Schluenzen F, Harms JM, Franceschi F, Hansen HA, Bartels H, Zarivach R, Yonath A. 2003. Structural basis for the antibiotic activity of ketolides and azalides. Structure 11: 329-338.
-
(2003)
Structure
, vol.11
, pp. 329-338
-
-
Schluenzen, F.1
Harms, J.M.2
Franceschi, F.3
Hansen, H.A.4
Bartels, H.5
Zarivach, R.6
Yonath, A.7
-
113
-
-
0035950132
-
Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria
-
Schluenzen F, Zarivach R, Harms J, Bashan A, Tocilj A, Albrecht R, Yonath A, Franceschi F. 2001. Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria. Nature 413: 814-821.
-
(2001)
Nature
, vol.413
, pp. 814-821
-
-
Schluenzen, F.1
Zarivach, R.2
Harms, J.3
Bashan, A.4
Tocilj, A.5
Albrecht, R.6
Yonath, A.7
Franceschi, F.8
-
114
-
-
34247242053
-
Structures of RNA switches: Insight into molecular recognition and tertiary structure
-
Schwalbe H, Buck J, Fürtig B, Noeske J, Wöhnert J. 2007. Structures of RNA switches: insight into molecular recognition and tertiary structure. Angew. Chem. Int. Ed. 46: 1212-1219.
-
(2007)
Angew. Chem. Int. Ed
, vol.46
, pp. 1212-1219
-
-
Schwalbe, H.1
Buck, J.2
Fürtig, B.3
Noeske, J.4
Wöhnert, J.5
-
115
-
-
4544340867
-
Monitoring molecular recognition of the ribosomal decoding site
-
Shandrick S, Zhao Q, Han Q, Ayida BK, Takahashi M, Winters GC, Simonsen KB, Vourloumis D, Hermann T. 2004. Monitoring molecular recognition of the ribosomal decoding site. Angew. Chem. Int. Ed. 43: 3177-3182.
-
(2004)
Angew. Chem. Int. Ed
, vol.43
, pp. 3177-3182
-
-
Shandrick, S.1
Zhao, Q.2
Han, Q.3
Ayida, B.K.4
Takahashi, M.5
Winters, G.C.6
Simonsen, K.B.7
Vourloumis, D.8
Hermann, T.9
-
116
-
-
54049112261
-
Rx-01: A new family of oxazolidinones that overcomes ribosomal-based linezolid resistance
-
Skripkin E, McConnell TS, Devito J, Lawrence L, Ippolito JA, Duffy EM, Sutcliffe J, Franceschi F. 2008. Rx-01: a new family of oxazolidinones that overcomes ribosomal-based linezolid resistance. Antimicrob. Agents Chemother. 52: 3550-3557.
-
(2008)
Antimicrob. Agents Chemother
, vol.52
, pp. 3550-3557
-
-
Skripkin, E.1
McConnell, T.S.2
Devito, J.3
Lawrence, L.4
Ippolito, J.A.5
Duffy, E.M.6
Sutcliffe, J.7
Franceschi, F.8
-
117
-
-
33748276474
-
Protein-ligand docking: Current status and future challenges
-
Sousa SF, Fernandes PA, Ramos MJ. 2006. Protein-ligand docking: current status and future challenges. Proteins 65: 15-26.
-
(2006)
Proteins
, vol.65
, pp. 15-26
-
-
Sousa, S.F.1
Fernandes, P.A.2
Ramos, M.J.3
-
118
-
-
0037442584
-
Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4
-
Spackova N, Cheatham TE, Ryjacek F, Lankas F, van Meervelt L, Hobza P, Sponer J. 2003. Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4' ',6-diamidino-2-phenylindole and DNA duplexes in solution. J. Am. Chem. Soc. 125: 1759-1769.
-
(2003)
, vol.125
, pp. 1759-1769
-
-
Spackova, N.1
Cheatham, T.E.2
Ryjacek, F.3
Lankas, F.4
van Meervelt, L.5
Hobza, P.6
Sponer, J.7
-
119
-
-
0345631645
-
Interaction between the guanine-cytosine Watson-Crick DNA base pair and hydrated group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and group IIb (Zn2+, Cd2+, Hg2+) metal cations
-
Sponer J, Burda JV, Sabat M, Leszczynski J, Hobza P. 1998. Interaction between the guanine-cytosine Watson-Crick DNA base pair and hydrated group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and group IIb (Zn2+, Cd2+, Hg2+) metal cations. J. Phys. Chem. A 102: 5951-5957.
-
(1998)
J. Phys. Chem. A
, vol.102
, pp. 5951-5957
-
-
Sponer, J.1
Burda, J.V.2
Sabat, M.3
Leszczynski, J.4
Hobza, P.5
-
120
-
-
33645326510
-
Nature of base stacking: Reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps
-
Sponer J, Jurecka P, Marchan I, Luque FJ, Orozco M, Hobza P. 2006. Nature of base stacking: reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps. Chemistry 12: 2854-2865.
-
(2006)
Chemistry
, vol.12
, pp. 2854-2865
-
-
Sponer, J.1
Jurecka, P.2
Marchan, I.3
Luque, F.J.4
Orozco, M.5
Hobza, P.6
-
121
-
-
20744441693
-
Principles of RNA base pairing: Structures and energies of the trans Watson-Crick/sugar edge base pairs
-
Sponer JE, Spackova N, Leszczynski J, Sponer J. 2005. Principles of RNA base pairing: structures and energies of the trans Watson-Crick/sugar edge base pairs. J. Phys. Chem. B 109: 11399-11410.
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 11399-11410
-
-
Sponer, J.E.1
Spackova, N.2
Leszczynski, J.3
Sponer, J.4
-
122
-
-
0032560959
-
Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate - DNA helices
-
Srinivasan J, Cheatham TE, Cieplak P, Kollman PA, Case DA. 1998. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate - DNA helices. J. Am. Chem. Soc. 120: 9401-9409.
-
(1998)
J. Am. Chem. Soc
, vol.120
, pp. 9401-9409
-
-
Srinivasan, J.1
Cheatham, T.E.2
Cieplak, P.3
Kollman, P.A.4
Case, D.A.5
-
123
-
-
0030324870
-
A docking and modelling strategy for peptide-RNA complexes: Applications to BIV Tat-TAR and HIV Rev-RBE
-
Srinivasan J, Leclerc F, Xu W, Ellington AD, Cedergren R. 1996. A docking and modelling strategy for peptide-RNA complexes: applications to BIV Tat-TAR and HIV Rev-RBE. Fold Des. 1: 463-472.
-
(1996)
Fold Des
, vol.1
, pp. 463-472
-
-
Srinivasan, J.1
Leclerc, F.2
Xu, W.3
Ellington, A.D.4
Cedergren, R.5
-
124
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still WC, Tempczyk A, Hawley RC, Hendrickson T. 1990. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 112: 6127-6129.
-
(1990)
J. Am. Chem. Soc
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
125
-
-
85011936087
-
Engineered riboswitches: Overview, problems and trends
-
Suess B, Weigand JE. 2008. Engineered riboswitches: overview, problems and trends. RNA Biology 5: 24-29.
-
(2008)
Rna Biology
, vol.5
, pp. 24-29
-
-
Suess, B.1
Weigand, J.E.2
-
126
-
-
25144480034
-
Improving on nature: Antibiotics that target the ribosome
-
Sutcliffe J. 2005. Improving on nature: antibiotics that target the ribosome. Curr. Opin. Microbiol. 8: 534-542.
-
(2005)
Curr. Opin. Microbiol
, vol.8
, pp. 534-542
-
-
Sutcliffe, J.1
-
127
-
-
0034308140
-
Building-block approach for determining low-frequency normal modes of macromolecules
-
Tama F, Gadea FX, Marques O, Sanejouand YH. 2000. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins 41: 1-7.
-
(2000)
Proteins
, vol.41
, pp. 1-7
-
-
Tama, F.1
Gadea, F.X.2
Marques, O.3
Sanejouand, Y.H.4
-
128
-
-
0035044995
-
Conformational change of proteins arising from normal mode calculations
-
Tama F, Sanejouand YH. 2001. Conformational change of proteins arising from normal mode calculations. Protein Eng. 14: 1-6.
-
(2001)
Protein Eng
, vol.14
, pp. 1-6
-
-
Tama, F.1
Sanejouand, Y.H.2
-
129
-
-
0042424707
-
Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
-
Tama F, Valle M, Frank J, Brooks CL. 2003. Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc. Natl. Acad. Sci. U.S.A. 100: 9319-9323.
-
(2003)
Proc. Natl. Acad. Sci. U.s.a
, vol.100
, pp. 9319-9323
-
-
Tama, F.1
Valle, M.2
Frank, J.3
Brooks, C.L.4
-
130
-
-
34547830982
-
Calculation of absolute free energy of binding for theophylline and its analogs to RNA aptamer using nonequilibrium work values
-
Tanida Y, Ito MS, Fujitani H. 2007. Calculation of absolute free energy of binding for theophylline and its analogs to RNA aptamer using nonequilibrium work values. Chem. Phys. 337: 135-143.
-
(2007)
Chem. Phys
, vol.337
, pp. 135-143
-
-
Tanida, Y.1
Ito, M.S.2
Fujitani, H.3
-
131
-
-
0036782103
-
Inhibitor binding alters the directions of domain motions in HIV-1 reverse transcriptase
-
Temiz NA, Bahar I. 2002. Inhibitor binding alters the directions of domain motions in HIV-1 reverse transcriptase. Proteins 49: 61-70.
-
(2002)
Proteins
, vol.49
, pp. 61-70
-
-
Temiz, N.A.1
Bahar, I.2
-
132
-
-
43149103943
-
Targeting RNA with small molecules
-
Thomas JR, Hergenrother PJ. 2008. Targeting RNA with small molecules. Chem. Rev. 108: 1171-1224.
-
(2008)
Chem. Rev
, vol.108
, pp. 1171-1224
-
-
Thomas, J.R.1
Hergenrother, P.J.2
-
133
-
-
33747891811
-
The ribosomal A-site as an inspiration for the design of RNA binders
-
Tor Y. 2006. The ribosomal A-site as an inspiration for the design of RNA binders. Biochimie 88: 1045-1051.
-
(2006)
Biochimie
, vol.88
, pp. 1045-1051
-
-
Tor, Y.1
-
134
-
-
17044393884
-
Coarse-grained models for proteins
-
Tozzini V. 2005. Coarse-grained models for proteins. Curr. Opin. Struct. Biol. 15: 144-150.
-
(2005)
Curr. Opin. Struct. Biol
, vol.15
, pp. 144-150
-
-
Tozzini, V.1
-
135
-
-
24144478280
-
Exploring global motions and correlations in the ribosome
-
Trylska J, Tozzini V, McCammon JA. 2005. Exploring global motions and correlations in the ribosome. Biophys. J. 89: 1455-1463.
-
(2005)
Biophys. J
, vol.89
, pp. 1455-1463
-
-
Trylska, J.1
Tozzini, V.2
McCammon, J.A.3
-
136
-
-
33747880625
-
A molecular dynamics simulation study of an aminoglycoside/A-site RNA complex: Conformational and hydration patterns
-
Vaiana AC, Westhof E, Auffinger P. 2006. A molecular dynamics simulation study of an aminoglycoside/A-site RNA complex: conformational and hydration patterns. Biochimie 88: 1061-1073.
-
(2006)
Biochimie
, vol.88
, pp. 1061-1073
-
-
Vaiana, A.C.1
Westhof, E.2
Auffinger, P.3
-
137
-
-
25844441847
-
Comparison of mode analyses at different resolutions applied to nucleic acid systems
-
Van Wynsberghe AW, Cui Q. 2005. Comparison of mode analyses at different resolutions applied to nucleic acid systems. Biophys. J. 89: 2939-2949.
-
(2005)
Biophys. J
, vol.89
, pp. 2939-2949
-
-
van Wynsberghe, A.W.1
Cui, Q.2
-
138
-
-
26444588137
-
DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction
-
Velec HF, Gohlke H, Klebe G. 2005. DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction. J. Med. Chem. 48: 6296-6303.
-
(2005)
J. Med. Chem
, vol.48
, pp. 6296-6303
-
-
Velec, H.F.1
Gohlke, H.2
Klebe, G.3
-
139
-
-
0142106950
-
RNA as a drug target: The case of aminoglycosides
-
Vicens Q, Westhof E. 2003. RNA as a drug target: the case of aminoglycosides. ChemBioChem 4: 1018-1023.
-
(2003)
Chembiochem
, vol.4
, pp. 1018-1023
-
-
Vicens, Q.1
Westhof, E.2
-
140
-
-
0033656867
-
In vitro selection and characterization of RNAs with high affinity to antibiotics
-
Wallace ST, Schroeder R. 2000. In vitro selection and characterization of RNAs with high affinity to antibiotics. Methods Enzymol. 318: 214-229.
-
(2000)
Methods Enzymol
, vol.318
, pp. 214-229
-
-
Wallace, S.T.1
Schroeder, R.2
-
141
-
-
4344685227
-
Global ribosome motions revealed with elastic network model
-
Wang Y, Rader AJ, Bahar I, Jernigan R. 2004. Global ribosome motions revealed with elastic network model. J. Struct. Biol. 147: 302-314.
-
(2004)
J. Struct. Biol
, vol.147
, pp. 302-314
-
-
Wang, Y.1
Rader, A.J.2
Bahar, I.3
Jernigan, R.4
-
142
-
-
36749024620
-
Polarizable force fields: History, test cases, and prospects
-
Warshel A, Kato M, Pisliakov AV. 2007. Polarizable force fields: history, test cases, and prospects. J. Chem. Theor. Comput. 3: 2034-2045.
-
(2007)
J. Chem. Theor. Comput
, vol.3
, pp. 2034-2045
-
-
Warshel, A.1
Kato, M.2
Pisliakov, A.V.3
-
143
-
-
0020475509
-
Calculation of the electric-potential in the active-site cleft due to alpha-helix dipoles
-
Warwicker J, Watson HC. 1982. Calculation of the electric-potential in the active-site cleft due to alpha-helix dipoles. J. Mol. Biol. 157: 671-679.
-
(1982)
J. Mol. Biol
, vol.157
, pp. 671-679
-
-
Warwicker, J.1
Watson, H.C.2
-
144
-
-
27744471408
-
Constrained geometric simulation of diffusive motion in proteins
-
Wells S, Menor S, Hespenheide B, Thorpe MF. 2005. Constrained geometric simulation of diffusive motion in proteins. Phys. Biol. 2: 127-136.
-
(2005)
Phys. Biol
, vol.2
, pp. 127-136
-
-
Wells, S.1
Menor, S.2
Hespenheide, B.3
Thorpe, M.F.4
-
145
-
-
0000521158
-
Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals
-
Westhof E, Dumas P, Moras D. 1988. Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals. Acta. Crystallogr. A 44 (Pt 2): 112-123.
-
(1988)
Acta. Crystallogr. A
, vol.44
, Issue.Pt 2
, pp. 112-123
-
-
Westhof, E.1
Dumas, P.2
Moras, D.3
-
146
-
-
51649117099
-
The oxazolidinone antibiotics perturb the ribosomal peptidyltransferase center and effect tRNA positioning
-
Wilson DN, Schluenzen F, Harms JM, Starosta AL, Connell SR, Fucini P. 2008. The oxazolidinone antibiotics perturb the ribosomal peptidyltransferase center and effect tRNA positioning. Proc. Natl Acad. Sci. U.S.A. 105: 13339-13344.
-
(2008)
Proc. Natl Acad. Sci. U.s.a
, vol.105
, pp. 13339-13344
-
-
Wilson, D.N.1
Schluenzen, F.2
Harms, J.M.3
Starosta, A.L.4
Connell, S.R.5
Fucini, P.6
-
147
-
-
33748568807
-
Binding of aminoglycosidic antibiotics to the oligonucleotide A-site model and 30S ribosomal subunit: Poisson-Boltzmann model, thermal denaturation, and fluorescence studies
-
Yang G, Trylska J, Tor Y, McCammon JA. 2006a. Binding of aminoglycosidic antibiotics to the oligonucleotide A-site model and 30S ribosomal subunit: Poisson-Boltzmann model, thermal denaturation, and fluorescence studies. J. Med. Chem. 49: 5478-5490.
-
(2006)
J. Med. Chem
, vol.49
, pp. 5478-5490
-
-
Yang, G.1
Trylska, J.2
Tor, Y.3
McCammon, J.A.4
-
148
-
-
33747829284
-
oGNM: Online computation of structural dynamics using the Gaussian network model
-
Yang LW, Rader AJ, Liu X, Jursa CJ, Chen SC, Karimi HA, Bahar I. 2006b. oGNM: online computation of structural dynamics using the Gaussian network model. Nucleic Acids Res. 34: W24-W31.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Yang, L.W.1
Rader, A.J.2
Liu, X.3
Jursa, C.J.4
Chen, S.C.5
Karimi, H.A.6
Bahar, I.7
-
149
-
-
0032538956
-
Structural origins of gentamicin antibiotic action
-
Yoshizawa S, Fourmy D, Puglisi JD. 1998. Structural origins of gentamicin antibiotic action. EMBO J. 17: 6437-6448.
-
(1998)
Embo J
, vol.17
, pp. 6437-6448
-
-
Yoshizawa, S.1
Fourmy, D.2
Puglisi, J.D.3
-
150
-
-
0034578639
-
Comparison of molecular dynamics and harmonic mode calculations on RNA
-
Zacharias M. 2000. Comparison of molecular dynamics and harmonic mode calculations on RNA. Biopolymers 54: 547-560.
-
(2000)
Biopolymers
, vol.54
, pp. 547-560
-
-
Zacharias, M.1
-
152
-
-
0034063442
-
Conformational deformability of RNA: A harmonic mode analysis
-
Zacharias M, Sklenar H. 2000. Conformational deformability of RNA: a harmonic mode analysis. Biophys. J. 78: 2528-2542.
-
(2000)
Biophys. J
, vol.78
, pp. 2528-2542
-
-
Zacharias, M.1
Sklenar, H.2
-
153
-
-
4544310320
-
Modeling correlated main-chain motions in proteins for flexible molecular recognition
-
Zavodszky MI, Ming L, Thorpe MF, Day AR, Kuhn LA. 2004. Modeling correlated main-chain motions in proteins for flexible molecular recognition. Proteins 57: 243-261.
-
(2004)
Proteins
, vol.57
, pp. 243-261
-
-
Zavodszky, M.I.1
Ming, L.2
Thorpe, M.F.3
Day, A.R.4
Kuhn, L.A.5
-
154
-
-
31944446215
-
Resolving the motional modes that code for RNA adaptation
-
Zhang Q, Sun X, Watt ED. Al-Hashimi HM. 2006. Resolving the motional modes that code for RNA adaptation. Science 311: 653-656.
-
(2006)
Science
, vol.311
, pp. 653-656
-
-
Zhang, Q.1
Sun, X.2
Al-Hashimi Watt, E.D.3
-
155
-
-
37549017736
-
Visualizing spatially correlated dynamics that directs RNA conformational transitions
-
Zhang Q, Stelzer A, Fisher C, Al-Hashimi H. 2007. Visualizing spatially correlated dynamics that directs RNA conformational transitions. Nature 450: 1263-1267.
-
(2007)
Nature
, vol.450
, pp. 1263-1267
-
-
Zhang, Q.1
Stelzer, A.2
Fisher, C.3
Al-Hashimi, H.4
-
156
-
-
49449086540
-
An improved PMF scoring function for universally predicting the interactions of a ligand with protein, DNA, and RNA
-
Zhao XY, Liu XF, Wang YY, Chen Z, Kang L, Zhang HL, Luo XM, Zhu WL, Chen KX, Li HL, Wang XC, Jiang HL. 2008. An improved PMF scoring function for universally predicting the interactions of a ligand with protein, DNA, and RNA. J. Chem. Inf. Mod. 48: 1438-1447.
-
(2008)
J. Chem. Inf. Mod
, vol.48
, pp. 1438-1447
-
-
Zhao, X.Y.1
Liu, X.F.2
Wang, Y.Y.3
Chen, Z.4
Kang, L.5
Zhang, H.L.6
Luo, X.M.7
Zhu, W.L.8
Chen, K.X.9
Li, H.L.10
Wang, X.C.11
Jiang, H.L.12
-
157
-
-
43849094020
-
A unification of the elastic network model and the Gaussian network model for optimal description of protein conformational motions and fluctuations
-
Zheng W. 2008. A unification of the elastic network model and the Gaussian network model for optimal description of protein conformational motions and fluctuations. Biophys. J. 94: 3853-3857.
-
(2008)
Biophys. J
, vol.94
, pp. 3853-3857
-
-
Zheng, W.1
-
158
-
-
0033536456
-
Inclusion of solvation in ligand binding free energy calculations using the generalized-born model
-
Zou XQ, Sun YX, Kuntz ID. 1999. Inclusion of solvation in ligand binding free energy calculations using the generalized-born model. J. Am. Chem. Soc. 121: 8033-8043.
-
(1999)
J. Am. Chem. Soc
, vol.121
, pp. 8033-8043
-
-
Zou, X.Q.1
Sun, Y.X.2
Kuntz, I.D.3
|