-
1
-
-
0029633168
-
Gromacs - A message-passing parallel moleculardynamics implementation
-
Berendsen, H. J. C. et al. (1995) Gromacs - a message-passing parallel moleculardynamics implementation. Comput. Phys. Commun. 91, 43-56
-
(1995)
Comput. Phys. Commun.
, vol.91
, pp. 43-56
-
-
Berendsen, H.J.C.1
-
2
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips, J. C. et al. (2005) Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781-1802
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
-
3
-
-
67650500988
-
CHARMM: The biomolecular simulation program
-
Brooks, B. R. et al. (2009) CHARMM: the biomolecular simulation program. J. Comput. Chem. 30, 1545-1614
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 1545-1614
-
-
Brooks, B.R.1
-
4
-
-
23444454552
-
The Amber biomolecular simulation programs
-
Case, D. A. et al. (2005) The Amber biomolecular simulation programs. J. Comput. Chem. 26, 1668-1688
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1668-1688
-
-
Case, D.A.1
-
5
-
-
84865383775
-
On developing coarse-grained models for biomolecular simulation: A review
-
Riniker, S. et al. (2012) On developing coarse-grained models for biomolecular simulation: a review. Phys. Chem. Chem. Phys. 14, 12423-12430
-
(2012)
Phys. Chem. Chem. Phys.
, vol.14
, pp. 12423-12430
-
-
Riniker, S.1
-
6
-
-
0017100947
-
Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
-
Warshel, A. and Levitt, M. (1976) Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol. 103, 227-249
-
(1976)
J. Mol. Biol.
, vol.103
, pp. 227-249
-
-
Warshel, A.1
Levitt, M.2
-
7
-
-
0038394717
-
Preface to proceedings of the symposium on methods and applications of combined quantum mechanical and molecular mechanical potentials (2001)
-
Gao, J. and York, D. (2003) Preface to proceedings of the symposium on methods and applications of combined quantum mechanical and molecular mechanical potentials (2001). Theor. Chem. Acc. 109, 99
-
(2003)
Theor. Chem. Acc.
, vol.109
, pp. 99
-
-
Gao, J.1
York, D.2
-
8
-
-
0345713551
-
Hybrid models for combined quantum mechanical and molecular mechanical approaches
-
Bakowies, D. and Thiel, W. (1996) Hybrid models for combined quantum mechanical and molecular mechanical approaches. J. Phys. Chem. 100, 10580-10594
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 10580-10594
-
-
Bakowies, D.1
Thiel, W.2
-
9
-
-
0035312820
-
New developments in applying quantum mechanics to proteins
-
Gogonea, V. et al. (2001) New developments in applying quantum mechanics to proteins. Curr. Opin. Struct. Biol. 11, 217-223
-
(2001)
Curr. Opin. Struct. Biol.
, vol.11
, pp. 217-223
-
-
Gogonea, V.1
-
10
-
-
84986513644
-
A combined quantum-mechanical and molecular mechanical potential for molecular-dynamics simulations
-
Field, M. J. et al. (1990) A combined quantum-mechanical and molecular mechanical potential for molecular-dynamics simulations. J. Comput. Chem. 11, 700-733
-
(1990)
J. Comput. Chem.
, vol.11
, pp. 700-733
-
-
Field, M.J.1
-
11
-
-
84873338486
-
Systematic coarse-graining methods for soft matter simulations - A review
-
Brini, E. et al. (2013) Systematic coarse-graining methods for soft matter simulations - a review. Soft Matter 9, 2108-2119
-
(2013)
Soft Matter
, vol.9
, pp. 2108-2119
-
-
Brini, E.1
-
12
-
-
84864755959
-
Structural effects of an atomic-level layer of water molecules around proteins solvated in supra-molecular coarse-grained water
-
Riniker, S. et al. (2012) Structural effects of an atomic-level layer of water molecules around proteins solvated in supra-molecular coarse-grained water. J. Phys. Chem. B 116, 8873-8879
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 8873-8879
-
-
Riniker, S.1
-
13
-
-
0001216964
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules (vol. 117, pg. 5179, 1995)
-
Cornell, W. D. et al. (1996) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules (vol. 117, pg. 5179, 1995). J. Am. Chem. Soc. 118, 2309
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 2309
-
-
Cornell, W.D.1
-
14
-
-
33645941402
-
The Opls potential functions for proteins-energy minimizations for crystals of cyclic-peptides and crambin
-
Jorgensen, W. L. and Tiradorives, J. (1988) The Opls potential functions for proteins-energy minimizations for crystals of cyclic-peptides and crambin. J. Am. Chem. Soc. 110, 1657-1666
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 1657-1666
-
-
Jorgensen, W.L.1
Tiradorives, J.2
-
15
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell, A. D. et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102, 3586-3616
-
(1998)
J. Phys. Chem.
, vol.B 102
, pp. 3586-3616
-
-
MacKerell, A.D.1
-
16
-
-
4444282928
-
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
-
Oostenbrink, C. et al. (2004) A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J. Comput. Chem. 25, 1656-1676
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1656-1676
-
-
Oostenbrink, C.1
-
17
-
-
11144347566
-
Development and testing of a general amber force field (vol. 25, pg. 1157, 2004)
-
Wang, J. M. et al. (2005) Development and testing of a general amber force field (vol. 25, pg. 1157, 2004). J. Comput. Chem. 26, 114
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 114
-
-
Wang, J.M.1
-
18
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
Jorgensen, W. L. et al. (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 118, 11225-11236
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
-
19
-
-
84871545594
-
Automation of the CHARMM general force field (CGenFF) I: Bond perception and atom typing
-
Vanommeslaeghe, K. and MacKerell, A. D. (2012) Automation of the CHARMM general force field (CGenFF) I: bond perception and atom typing. J. Chem. Inf. Model. 52, 3144-3154
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 3144-3154
-
-
Vanommeslaeghe, K.1
MacKerell, A.D.2
-
20
-
-
84871544678
-
Automation of the CHARMM general force field (CGenFF) II: Assignment of bonded parameters and partial atomic charges
-
Vanommeslaeghe, K. et al. (2012) Automation of the CHARMM general force field (CGenFF) II: assignment of bonded parameters and partial atomic charges. J. Chem. Inf. Model. 52, 3155-3168
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 3155-3168
-
-
Vanommeslaeghe, K.1
-
21
-
-
84961981789
-
An automated force field topology builder (ATB) and repository: Version 1.0
-
Malde, A. K. et al. (2011) An automated force field topology builder (ATB) and repository: version 1.0. J. Chem. Theory Comput. 7, 4026-4037
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 4026-4037
-
-
Malde, A.K.1
-
22
-
-
33646471468
-
Statistical mechanics of fluid mixtures
-
Kirkwood, J. G. (1935) Statistical mechanics of fluid mixtures. J. Chem. Phys. 3, 300-313
-
(1935)
J. Chem. Phys.
, vol.3
, pp. 300-313
-
-
Kirkwood, J.G.1
-
23
-
-
1842854171
-
Statistical mechanical theory of transport processes. 7. The coefficient of thermal conductivity of monatomic liquids
-
Zwanzig, R. W. et al. (1954) Statistical mechanical theory of transport processes. 7. The coefficient of thermal conductivity of monatomic liquids. J. Chem. Phys. 22, 783-790
-
(1954)
J. Chem. Phys.
, vol.22
, pp. 783-790
-
-
Zwanzig, R.W.1
-
24
-
-
5244304444
-
Efficient estimation of free-energy differences from Monte-Carlo data
-
Bennett, C. H. (1976) Efficient estimation of free-energy differences from Monte-Carlo data. J. Comput. Phys. 22, 245-268
-
(1976)
J. Comput. Phys.
, vol.22
, pp. 245-268
-
-
Bennett, C.H.1
-
25
-
-
0031637651
-
Ligand binding affinity prediction by linear interaction energy methods
-
Hansson, T. et al. (1998) Ligand binding affinity prediction by linear interaction energy methods. J. Comput. Aided Mol. Des. 12, 27-35
-
(1998)
J. Comput. Aided Mol. Des.
, vol.12
, pp. 27-35
-
-
Hansson, T.1
-
26
-
-
33748637571
-
Recent advances in free energy calculations with a combination of molecular mechanics and continuum models
-
Wang, J. M. et al. (2006) Recent advances in free energy calculations with a combination of molecular mechanics and continuum models. Curr. Comput. Aided Drug Des. 2, 287-306
-
(2006)
Curr. Comput. Aided Drug Des.
, vol.2
, pp. 287-306
-
-
Wang, J.M.1
-
27
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
-
Kollman, P. A. et al. (2000) Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc. Chem. Res. 33, 889-897
-
(2000)
Acc. Chem. Res.
, vol.33
, pp. 889-897
-
-
Kollman, P.A.1
-
28
-
-
58149327312
-
Animproved methodto predict the entropy term with the MM/PBSA approach
-
Kongsted, J. and Ryde, U. (2009) Animproved methodto predict the entropy term with the MM/PBSA approach. J. Comput. Aided Mol. Des. 23, 63-71
-
(2009)
J. Comput. Aided Mol. Des.
, vol.23
, pp. 63-71
-
-
Kongsted, J.1
Ryde, U.2
-
29
-
-
34147177151
-
Improved sampling methods for molecular simulation
-
Lei, H. X. and Duan, Y. (2007) Improved sampling methods for molecular simulation. Curr. Opin. Struct. Biol. 17, 187-191
-
(2007)
Curr. Opin. Struct. Biol.
, vol.17
, pp. 187-191
-
-
Lei, H.X.1
Duan, Y.2
-
30
-
-
79960357485
-
Assessing protein kinase selectivity with molecular dynamics and MM-PBSA bindingfree energy calculations
-
Muzzioli, E. et al. (2011) Assessing protein kinase selectivity with molecular dynamics and MM-PBSA bindingfree energy calculations. Chem. Biol. Drug Des. 78, 252-259
-
(2011)
Chem. Biol. Drug Des.
, vol.78
, pp. 252-259
-
-
Muzzioli, E.1
-
31
-
-
84866410557
-
Exploring the selectivity of a ligand complex with CDK2/CDK1: A molecular dynamics simulation approach
-
Tripathi, S. K. et al. (2012) Exploring the selectivity of a ligand complex with CDK2/CDK1: a molecular dynamics simulation approach. J. Mol. Recognit. 25, 504-512
-
(2012)
J. Mol. Recognit.
, vol.25
, pp. 504-512
-
-
Tripathi, S.K.1
-
32
-
-
84880286488
-
Extra precision docking, free energy calculation and molecular dynamics simulation studies of CDK2 inhibitors
-
Tripathi, S. K. et al. (2013) Extra precision docking, free energy calculation and molecular dynamics simulation studies of CDK2 inhibitors. J. Theor. Biol. 334, 87-100
-
(2013)
J. Theor. Biol.
, vol.334
, pp. 87-100
-
-
Tripathi, S.K.1
-
33
-
-
84894684164
-
Steered molecular dynamics simulations for studying protein-ligand interaction in cyclin-dependent kinase 5
-
Patel, J. S. et al. (2014) Steered molecular dynamics simulations for studying protein-ligand interaction in cyclin-dependent kinase 5. J. Chem. Inf. Model. 54, 470-480
-
(2014)
J. Chem. Inf. Model.
, vol.54
, pp. 470-480
-
-
Patel, J.S.1
-
34
-
-
84877122657
-
Computational study of EGFR inhibition: Molecular dynamics studies on the active and inactive protein conformations
-
Songtawee, N. et al. (2013) Computational study of EGFR inhibition: molecular dynamics studies on the active and inactive protein conformations. J. Mol. Model. 19, 497-509
-
(2013)
J. Mol. Model.
, vol.19
, pp. 497-509
-
-
Songtawee, N.1
-
35
-
-
84906237552
-
Conformational transition pathways of epidermal growth factor receptor kinase domain from multiple molecular dynamics simulations and Bayesian clustering
-
Li, Y. et al. (2014) Conformational transition pathways of epidermal growth factor receptor kinase domain from multiple molecular dynamics simulations and Bayesian clustering. J. Chem. Theory Comput. 10, 3503-3511
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 3503-3511
-
-
Li, Y.1
-
36
-
-
84919832780
-
Activation pathway of Src kinase reveals intermediate states as targets for drug design
-
Shukla, D. et al. (2014) Activation pathway of Src kinase reveals intermediate states as targets for drug design. Nat. Commun. 5, 3397
-
(2014)
Nat. Commun.
, vol.5
, pp. 3397
-
-
Shukla, D.1
-
37
-
-
79958799244
-
Ligand chirality effects on the dynamics of human 3-phosphoglycerate kinase: Comparison between d- and l-nucleotides
-
Palmai, Z. et al. (2011) Ligand chirality effects on the dynamics of human 3-phosphoglycerate kinase: comparison between d- and l-nucleotides. Arch. Biochem. Biophys. 511, 88-100
-
(2011)
Arch. Biochem. Biophys.
, vol.511
, pp. 88-100
-
-
Palmai, Z.1
-
38
-
-
84871836555
-
Allosteric networks in thrombin distinguish procoagulant vs. Anticoagulant activities
-
Gasper, P. M. et al. (2012) Allosteric networks in thrombin distinguish procoagulant vs. anticoagulant activities. Proc. Natl. Acad. Sci. U. S. A. 109, 21216-21222
-
(2012)
Proc. Natl. Acad. Sci. U. S. A.
, vol.109
, pp. 21216-21222
-
-
Gasper, P.M.1
-
39
-
-
84886671844
-
Correlated motions and residual frustration in thrombin
-
Fuglestad, B. et al. (2013) Correlated motions and residual frustration in thrombin. J. Phys. Chem. B 117, 12857-12863
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 12857-12863
-
-
Fuglestad, B.1
-
40
-
-
84887435369
-
Molecular dynamics simulation and molecular docking studies of angiotensin converting enzyme with inhibitor lisinopril and amyloid beta peptide
-
Jalkute, C. B. et al. (2013) Molecular dynamics simulation and molecular docking studies of angiotensin converting enzyme with inhibitor lisinopril and amyloid beta peptide. Protein J. 32, 356-364
-
(2013)
Protein J.
, vol.32
, pp. 356-364
-
-
Jalkute, C.B.1
-
41
-
-
84864660051
-
Understanding the basis of drug resistance of the mutants of alpha beta-tubulin dimer via molecular dynamics simulations
-
Natarajan, K. and Senapati, S. (2012) Understanding the basis of drug resistance of the mutants of alpha beta-tubulin dimer via molecular dynamics simulations. PLoS ONE 7, e42351
-
(2012)
PLoS ONE
, vol.7
, pp. e42351
-
-
Natarajan, K.1
Senapati, S.2
-
42
-
-
84863126869
-
Exploring inhibitor release pathways in histone deacetylases using random acceleration molecular dynamics simulations
-
Kalyaanamoorthy, S. and Chen, Y. P. P. (2012) Exploring inhibitor release pathways in histone deacetylases using random acceleration molecular dynamics simulations. J. Chem. Inf. Model. 52, 589-603
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 589-603
-
-
Kalyaanamoorthy, S.1
Chen, Y.P.P.2
-
43
-
-
84871976247
-
Structural and dynamic basis of human cytochrome P4507B1: A survey of substrate selectivity and major active site access channels
-
Cui, Y. L. et al. (2013) Structural and dynamic basis of human cytochrome P4507B1: a survey of substrate selectivity and major active site access channels. Chemistry 19, 548-556
-
(2013)
Chemistry
, vol.19
, pp. 548-556
-
-
Cui, Y.L.1
-
44
-
-
84862884578
-
Cytochrome P450 3A4 inhibition by ketoconazole: Tackling the problem of ligand cooperativity using molecular dynamics simulations and free-energy calculations
-
Bren, U. and Oostenbrink, C. (2012) Cytochrome P450 3A4 inhibition by ketoconazole: tackling the problem of ligand cooperativity using molecular dynamics simulations and free-energy calculations. J. Chem. Inf. Model. 52, 1573-1582
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 1573-1582
-
-
Bren, U.1
Oostenbrink, C.2
-
45
-
-
79954997862
-
Understanding the determinants of selectivity in drug metabolism through modeling of dextromethorphan oxidation by cytochrome P450
-
Olah, J. et al. (2011) Understanding the determinants of selectivity in drug metabolism through modeling of dextromethorphan oxidation by cytochrome P450. Proc. Natl. Acad. Sci. U. S. A. 108, 6050-6055
-
(2011)
Proc. Natl. Acad. Sci. U. S. A.
, vol.108
, pp. 6050-6055
-
-
Olah, J.1
-
46
-
-
80053305889
-
Does compound I vary significantly between isoforms of cytochrome P450?
-
Lonsdale, R. et al. (2011) Does compound I vary significantly between isoforms of cytochrome P450? J. Am. Chem. Soc. 133, 15464-15474
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 15464-15474
-
-
Lonsdale, R.1
-
47
-
-
84889037440
-
High accuracy in silico sulfotransferase models
-
Cook, I. et al. (2013) High accuracy in silico sulfotransferase models. J. Biol. Chem. 288, 34494-34501
-
(2013)
J. Biol. Chem.
, vol.288
, pp. 34494-34501
-
-
Cook, I.1
-
48
-
-
84883622106
-
In silico mechanistic profiling to probe small molecule binding to sulfotransferases
-
Martiny, V. Y. et al. (2013) In silico mechanistic profiling to probe small molecule binding to sulfotransferases. PLoS ONE 8, e73587
-
(2013)
PLoS ONE
, vol.8
, pp. e73587
-
-
Martiny, V.Y.1
-
49
-
-
84872506191
-
The gate that governs sulfotransferase selectivity
-
Cook, I. et al. (2013) The gate that governs sulfotransferase selectivity. Biochemistry 52, 415-424
-
(2013)
Biochemistry
, vol.52
, pp. 415-424
-
-
Cook, I.1
-
50
-
-
78651399683
-
Structure and function of an irreversible agonistbeta (2) adrenoceptor complex
-
Rosenbaum, D. M. et al. (2011) Structure and function of an irreversible agonistbeta (2) adrenoceptor complex. Nature 469, 236-240
-
(2011)
Nature
, vol.469
, pp. 236-240
-
-
Rosenbaum, D.M.1
-
51
-
-
81755163613
-
Activation mechanism of the β2-adrenergic receptor
-
Dror, R. O. et al. (2011) Activation mechanism of the β2-adrenergic receptor. Proc. Natl. Acad. Sci. U. S. A. 108, 18684-18689
-
(2011)
Proc. Natl. Acad. Sci. U. S. A.
, vol.108
, pp. 18684-18689
-
-
Dror, R.O.1
-
52
-
-
84873298278
-
The dynamic process of β (2)-adrenergic receptor activation
-
Nygaard, R. et al. (2013) The dynamic process of β (2)-adrenergic receptor activation. Cell 152, 532-542
-
(2013)
Cell
, vol.152
, pp. 532-542
-
-
Nygaard, R.1
-
53
-
-
80052001378
-
Pathway and mechanism of drug binding to G-proteincoupled receptors
-
Dror, R. O. et al. (2011) Pathway and mechanism of drug binding to G-proteincoupled receptors. Proc. Natl. Acad. Sci. U. S. A. 108, 13118-13123
-
(2011)
Proc. Natl. Acad. Sci. U. S. A.
, vol.108
, pp. 13118-13123
-
-
Dror, R.O.1
-
54
-
-
84863115467
-
Structure and dynamics of the M3 muscarinic acetylcholine receptor
-
Kruse, A. C. et al. (2012) Structure and dynamics of the M3 muscarinic acetylcholine receptor. Nature 482, 552-556
-
(2012)
Nature
, vol.482
, pp. 552-556
-
-
Kruse, A.C.1
-
55
-
-
84906080911
-
Dualsteric muscarinic antagonists-orthosteric binding pose controls allosteric subtype selectivity
-
Schmitz, J. et al. (2014) Dualsteric muscarinic antagonists-orthosteric binding pose controls allosteric subtype selectivity. J. Med. Chem. 57, 6739-6750
-
(2014)
J. Med. Chem.
, vol.57
, pp. 6739-6750
-
-
Schmitz, J.1
-
56
-
-
79952125277
-
Predicted structures and dynamics for agonists and antagonists bound to serotonin 5-HT2B and 5-HT2C receptors
-
Kim, S.-K. et al. (2011) Predicted structures and dynamics for agonists and antagonists bound to serotonin 5-HT2B and 5-HT2C receptors. J. Chem. Inf. Model. 51, 420-433
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 420-433
-
-
Kim, S.-K.1
-
57
-
-
84861337783
-
Substrate binding and translocation of the serotonin transporter studiedby docking and molecular dynamics simulations
-
Gabrielsen, M. et al. (2012) Substrate binding and translocation of the serotonin transporter studiedby docking and molecular dynamics simulations. J. Mol. Model. 18, 1073-1085
-
(2012)
J. Mol. Model.
, vol.18
, pp. 1073-1085
-
-
Gabrielsen, M.1
-
58
-
-
84861666297
-
Delineation of the unbinding pathway of alpha-conotoxin Iml from the alpha 7 nicotinic acetylcholine receptor
-
Yu, R. et al. (2012) Delineation of the unbinding pathway of alpha-conotoxin Iml from the alpha 7 nicotinic acetylcholine receptor. J. Phys. Chem. B 116, 6097-6105
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 6097-6105
-
-
Yu, R.1
-
59
-
-
84875639205
-
The gating mechanism of the human aquaporin 5 revealed by molecular dynamics simulations
-
Janosi, L. and Ceccarelli, M. (2013) The gating mechanism of the human aquaporin 5 revealed by molecular dynamics simulations. PLoS ONE 8, e59897
-
(2013)
PLoS ONE
, vol.8
, pp. e59897
-
-
Janosi, L.1
Ceccarelli, M.2
-
60
-
-
84862203273
-
Insights on P-glycoprotein's efflux mechanism obtained by molecular dynamics simulations
-
Ferreira, R. J. et al. (2012) Insights on P-glycoprotein's efflux mechanism obtained by molecular dynamics simulations. J. Chem. Theory Comput. 8, 1853-1864
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 1853-1864
-
-
Ferreira, R.J.1
-
61
-
-
84873292211
-
Architecture and membrane interactions of the EGF receptor
-
Arkhipov, A. et al. (2013) Architecture and membrane interactions of the EGF receptor. Cell 152, 557-569
-
(2013)
Cell
, vol.152
, pp. 557-569
-
-
Arkhipov, A.1
-
62
-
-
84868585563
-
Another brick in the wall. Validation of the sigma (1) receptor 3D model by computer-assisted design, synthesis, and activity of new sigma (1) ligands
-
Laurini, E. et al. (2012) Another brick in the wall. Validation of the sigma (1) receptor 3D model by computer-assisted design, synthesis, and activity of new sigma (1) ligands. Mol. Pharm. 9, 3107-3126
-
(2012)
Mol. Pharm.
, vol.9
, pp. 3107-3126
-
-
Laurini, E.1
-
63
-
-
84884235713
-
Unbinding pathways from the glucocorticoid receptor shed light on the reduced sensitivity of glucocorticoid ligands to a naturally occurring, clinically relevant mutant receptor
-
Capelli, A. M. et al. (2013) Unbinding pathways from the glucocorticoid receptor shed light on the reduced sensitivity of glucocorticoid ligands to a naturally occurring, clinically relevant mutant receptor. J. Med. Chem. 56, 7003-7014
-
(2013)
J. Med. Chem.
, vol.56
, pp. 7003-7014
-
-
Capelli, A.M.1
-
64
-
-
84864976082
-
GQ-16, a novel peroxisome proliferator-activated receptor gamma (PPAR gamma) ligand, promotes insulin sensitization without weight gain
-
Amato, A. A. et al. (2012) GQ-16, a novel peroxisome proliferator-activated receptor gamma (PPAR gamma) ligand, promotes insulin sensitization without weight gain. J. Biol. Chem. 287, 28169-28179
-
(2012)
J. Biol. Chem.
, vol.287
, pp. 28169-28179
-
-
Amato, A.A.1
-
65
-
-
80052020054
-
Molecular dynamics simulation and binding energy calculation for estimation of oligonucleotide duplex thermostabilityin RNA-based therapeutics
-
Shen, L. et al. (2011) Molecular dynamics simulation and binding energy calculation for estimation of oligonucleotide duplex thermostabilityin RNA-based therapeutics. J. Chem. Inf. Model. 51, 1957-1965
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 1957-1965
-
-
Shen, L.1
-
66
-
-
84861393827
-
Multistep drug intercalation: Molecular dynamics and free energy studies of the binding of daunomycin to DNA
-
Wilhelm, M. et al. (2012) Multistep drug intercalation: molecular dynamics and free energy studies of the binding of daunomycin to DNA. J. Am. Chem. Soc. 134, 8588-8596
-
(2012)
J. Am. Chem. Soc.
, vol.134
, pp. 8588-8596
-
-
Wilhelm, M.1
-
67
-
-
84867427868
-
Early stage intercalation of doxorubicin to DNA fragments observed in molecular dynamics binding simulations
-
Lei, H. et al. (2012) Early stage intercalation of doxorubicin to DNA fragments observed in molecular dynamics binding simulations. J. Mol. Graph. Model. 38, 279-289
-
(2012)
J. Mol. Graph. Model.
, vol.38
, pp. 279-289
-
-
Lei, H.1
-
68
-
-
80055094035
-
Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities
-
Dolenc, J. et al. (2011) Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities. J. Comput. Aided Mol. Des. 25, 709-716
-
(2011)
J. Comput. Aided Mol. Des.
, vol.25
, pp. 709-716
-
-
Dolenc, J.1
-
69
-
-
80255136323
-
Identification of nonplanar small molecule for G-quadruplex grooves: Molecular docking and molecular dynamic study
-
Li, J. et al. (2011) Identification of nonplanar small molecule for G-quadruplex grooves: molecular docking and molecular dynamic study. Bioorg. Med. Chem. Lett. 21, 6969-6972
-
(2011)
Bioorg. Med. Chem. Lett.
, vol.21
, pp. 6969-6972
-
-
Li, J.1
-
70
-
-
80052229107
-
Impact of planarity of unfused aromatic molecules on G-quadruplex binding: Learning from isaindigotone derivatives
-
Hou, J. Q. et al. (2011) Impact of planarity of unfused aromatic molecules on G-quadruplex binding: learning from isaindigotone derivatives. Org. Biomol. Chem. 9, 6422-6436
-
(2011)
Org. Biomol. Chem.
, vol.9
, pp. 6422-6436
-
-
Hou, J.Q.1
-
71
-
-
84855196452
-
Binding of novel fullerene inhibitors to HIV-1 protease: Insight through molecular dynamics and molecular mechanics Poisson-Boltzmann surface area calculations
-
Tzoupis, H. et al. (2011) Binding of novel fullerene inhibitors to HIV-1 protease: insight through molecular dynamics and molecular mechanics Poisson-Boltzmann surface area calculations. J. Comput. Aided Mol. Des. 25, 959-976
-
(2011)
J. Comput. Aided Mol. Des.
, vol.25
, pp. 959-976
-
-
Tzoupis, H.1
-
72
-
-
84862833913
-
Computational studies of darunavir into HIV-1 protease and DMPC bilayer: Necessary conditions for effective binding and the role of the flaps
-
Leonis, G. et al. (2012) Computational studies of darunavir into HIV-1 protease and DMPC bilayer: necessary conditions for effective binding and the role of the flaps. J. Chem. Inf. Model. 52, 1542-1558
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 1542-1558
-
-
Leonis, G.1
-
73
-
-
84860733278
-
How does darunavir prevent HIV-1 protease dimerization?
-
Huang, D. Z. and Caflisch, A. (2012) How does darunavir prevent HIV-1 protease dimerization? J. Chem. Theory Comput. 8, 1786-1794
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 1786-1794
-
-
Huang, D.Z.1
Caflisch, A.2
-
74
-
-
84883231678
-
A contribution to the drug resistance mechanism of darunavir, amprenavir, indinavir, and saquinavir complexes with HIV-1 protease due to flap mutation I50V: A systematic MM-PBSA and thermodynamic integration study
-
Leonis, G. et al. (2013) A contribution to the drug resistance mechanism of darunavir, amprenavir, indinavir, and saquinavir complexes with HIV-1 protease due to flap mutation I50V: a systematic MM-PBSA and thermodynamic integration study. J. Chem. Inf. Model. 53, 2141-2153
-
(2013)
J. Chem. Inf. Model.
, vol.53
, pp. 2141-2153
-
-
Leonis, G.1
-
75
-
-
84864712248
-
Thumbs down for HIV: Domain level rearrangements do occur in the NNRTI-bound HIV-1 reverse transcriptase
-
Wright, D. W. et al. (2012) Thumbs down for HIV: domain level rearrangements do occur in the NNRTI-bound HIV-1 reverse transcriptase. J. Am. Chem. Soc. 134, 12885-12888
-
(2012)
J. Am. Chem. Soc.
, vol.134
, pp. 12885-12888
-
-
Wright, D.W.1
-
76
-
-
84865454171
-
Theoretical studies of HIV-1 reverse transcriptase inhibition
-
Swiderek, K. et al. (2012) Theoretical studies of HIV-1 reverse transcriptase inhibition. Phys. Chem. Chem. Phys. 14, 12614-12624
-
(2012)
Phys. Chem. Chem. Phys.
, vol.14
, pp. 12614-12624
-
-
Swiderek, K.1
-
77
-
-
84856226122
-
Molecular mechanism of HIV-1 integrase-vDNA interactions and strand transfer inhibitor action: A molecular modeling perspective
-
Xue, W. W. et al. (2012) Molecular mechanism of HIV-1 integrase-vDNA interactions and strand transfer inhibitor action: a molecular modeling perspective. J. Comput. Chem. 33, 527-536
-
(2012)
J. Comput. Chem.
, vol.33
, pp. 527-536
-
-
Xue, W.W.1
-
78
-
-
79955870873
-
Binding modes of diketo-acid inhibitors of HIV-1 integrase: A comparative molecular dynamics simulation study
-
Huang, M. et al. (2011) Binding modes of diketo-acid inhibitors of HIV-1 integrase: a comparative molecular dynamics simulation study. J. Mol. Graph. Model. 29, 956-964
-
(2011)
J. Mol. Graph. Model.
, vol.29
, pp. 956-964
-
-
Huang, M.1
-
79
-
-
84873025050
-
Exploring the molecular mechanism of cross-resistance to HIV-1 integrase strand transfer inhibitors by molecular dynamics simulation and residue interaction network analysis
-
Xue, W. et al. (2013) Exploring the molecular mechanism of cross-resistance to HIV-1 integrase strand transfer inhibitors by molecular dynamics simulation and residue interaction network analysis. J. Chem. Inf. Model. 53, 210-222
-
(2013)
J. Chem. Inf. Model.
, vol.53
, pp. 210-222
-
-
Xue, W.1
-
80
-
-
80053963569
-
An optimized MM/PBSA virtual screening approach applied to an HIV-1 gp41 fusion peptide inhibitor
-
Venken, T. et al. (2011) An optimized MM/PBSA virtual screening approach applied to an HIV-1 gp41 fusion peptide inhibitor. Proteins-Struct. Funct. Bioinform. 79, 3221-3235
-
(2011)
Proteins-struct. Funct. Bioinform.
, vol.79
, pp. 3221-3235
-
-
Venken, T.1
-
81
-
-
84878381053
-
Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics
-
Zhao, G. et al. (2013) Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature 497, 643-646
-
(2013)
Nature
, vol.497
, pp. 643-646
-
-
Zhao, G.1
-
82
-
-
84908089880
-
GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting
-
Stone, J. E. et al. (2014) GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting. Faraday Discuss. 169, 265-283
-
(2014)
Faraday Discuss.
, vol.169
, pp. 265-283
-
-
Stone, J.E.1
-
83
-
-
84867759741
-
Theoretical studies on the susceptibility of oseltamivir against variants of 2009 A/H1N1 influenza neuraminidase
-
Li, L. et al. (2012) Theoretical studies on the susceptibility of oseltamivir against variants of 2009 A/H1N1 influenza neuraminidase. J. Chem. Inf. Model. 52, 2715-2729
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 2715-2729
-
-
Li, L.1
-
84
-
-
84906938135
-
Inhibitory potency of flavonoid derivatives on influenza virus neuraminidase
-
Rakers, C. et al. (2014) Inhibitory potency of flavonoid derivatives on influenza virus neuraminidase. Bioorg. Med. Chem. Lett. 24, 4312-4317
-
(2014)
Bioorg. Med. Chem. Lett.
, vol.24
, pp. 4312-4317
-
-
Rakers, C.1
-
85
-
-
84887591023
-
Analysis and assay of oseltamivir-resistant mutants of influenza neuraminidase via direct observation of drug unbinding and rebinding in simulation
-
Woods, C. J. et al. (2013) Analysis and assay of oseltamivir-resistant mutants of influenza neuraminidase via direct observation of drug unbinding and rebinding in simulation. Biochemistry 52, 8150-8164
-
(2013)
Biochemistry
, vol.52
, pp. 8150-8164
-
-
Woods, C.J.1
-
86
-
-
79959520070
-
How do aminoadamantanes block the influenza M2 channel, and how does resistance develop?
-
Leonov, H. et al. (2011) How do aminoadamantanes block the influenza M2 channel, and how does resistance develop? J. Am. Chem. Soc. 133, 9903-9911
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 9903-9911
-
-
Leonov, H.1
-
87
-
-
84863351272
-
Ketoamide resistance and hepatitis C virus fitness in Val55 variants of the NS3 serine protease
-
Welsch, C. et al. (2012) Ketoamide resistance and hepatitis C virus fitness in Val55 variants of the NS3 serine protease. Antimicrob. Agents Chemother. 56, 1907-1915
-
(2012)
Antimicrob. Agents Chemother.
, vol.56
, pp. 1907-1915
-
-
Welsch, C.1
-
88
-
-
84888628148
-
Detailed computational study of the active site of the hepatitis C viral RNA polymerase to aid novel drug design
-
Barakat, K. H. et al. (2013) Detailed computational study of the active site of the hepatitis C viral RNA polymerase to aid novel drug design. J. Chem. Inf. Model. 53, 3031-3043
-
(2013)
J. Chem. Inf. Model.
, vol.53
, pp. 3031-3043
-
-
Barakat, K.H.1
-
89
-
-
84857521070
-
Multiple keys for a single lock: The unusual structural plasticity of the nucleotidyltransferase (4')/kanamycin complex
-
Matesanz, R. et al. (2012) Multiple keys for a single lock: the unusual structural plasticity of the nucleotidyltransferase (4')/kanamycin complex. Chemistry 18, 2875-2889
-
(2012)
Chemistry
, vol.18
, pp. 2875-2889
-
-
Matesanz, R.1
-
90
-
-
84865704280
-
Unidirectional peristaltic movement in multisite drug binding pockets of AcrB from molecular dynamics simulations
-
Feng, Z. et al. (2012) Unidirectional peristaltic movement in multisite drug binding pockets of AcrB from molecular dynamics simulations. Mol. Biosyst. 8, 2699-2709
-
(2012)
Mol. Biosyst.
, vol.8
, pp. 2699-2709
-
-
Feng, Z.1
-
91
-
-
34249904963
-
Targeted molecular dynamics simulation studies of binding and conformational changes in E-coli MurD
-
Perdih, A. et al. (2007) Targeted molecular dynamics simulation studies of binding and conformational changes in E-coli MurD. Proteins-Struct. Funct. Bioinform. 68, 243-254
-
(2007)
Proteins-struct. Funct. Bioinform.
, vol.68
, pp. 243-254
-
-
Perdih, A.1
-
92
-
-
84555223675
-
MurD ligase from Escherichia coli: C-terminal domain closing motion
-
Perdih, A. and Solmajer, T. (2012) MurD ligase from Escherichia coli: C-terminal domain closing motion. Comput. Theor. Chem. 979, 73-81
-
(2012)
Comput. Theor. Chem.
, vol.979
, pp. 73-81
-
-
Perdih, A.1
Solmajer, T.2
-
93
-
-
84901599414
-
Inhibitor design strategy based on an enzyme structural flexibility: A case of bacterial MurD ligase
-
Perdih, A. et al. (2014) Inhibitor design strategy based on an enzyme structural flexibility: a case of bacterial MurD ligase. J. Chem. Inf. Model. 54, 1451-1466
-
(2014)
J. Chem. Inf. Model.
, vol.54
, pp. 1451-1466
-
-
Perdih, A.1
-
94
-
-
84899111509
-
A structural and energetic model for the slow-onset inhibition of the Mycobacterium tuberculosis Enoyl-ACP reductase InhA
-
Li, H. J. et al. (2014) A structural and energetic model for the slow-onset inhibition of the Mycobacterium tuberculosis Enoyl-ACP reductase InhA. ACS Chem. Biol. 9, 986-993
-
(2014)
ACS Chem. Biol.
, vol.9
, pp. 986-993
-
-
Li, H.J.1
-
95
-
-
84861226790
-
Conformational changes in 2-trans-enoyl-ACP (CoA)
-
Da Costa, A. L. P. et al. (2012) Conformational changes in 2-trans-enoyl-ACP (CoA) reductase (InhA) from M. tuberculosis induced by an inorganic complex: a molecular dynamics simulation study. J. Mol. Model. 18, 1779-1790
-
(2012)
Reductase (InhA)
, vol.18
, pp. 1779-1790
-
-
Da Costa, A.L.P.1
-
96
-
-
84904397809
-
Structural insight into exosite binding and discovery of novel exosite inhibitors of botulinum neurotoxin serotype A through in silico screening
-
Hu, X. et al. (2014) Structural insight into exosite binding and discovery of novel exosite inhibitors of botulinum neurotoxin serotype A through in silico screening. J. Comput. Aided Mol. Des. 28, 765-778
-
(2014)
J. Comput. Aided Mol. Des.
, vol.28
, pp. 765-778
-
-
Hu, X.1
-
97
-
-
84861511519
-
Elements of nucleotide specificity in the Trypanosoma brucei mitochondrial RNA editing enzyme RET2
-
Demir, O. and Amaro, R. E. (2012) Elements of nucleotide specificity in the Trypanosoma brucei mitochondrial RNA editing enzyme RET2. J. Chem. Inf. Model. 52, 1308-1318
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 1308-1318
-
-
Demir, O.1
Amaro, R.E.2
-
98
-
-
84901417389
-
Quantum mechanics/molecular mechanics studies of the mechanism of falcipain-2 inhibition by the epoxysuccinate E64
-
Arafet, K. et al. (2014) Quantum mechanics/molecular mechanics studies of the mechanism of falcipain-2 inhibition by the epoxysuccinate E64. Biochemistry 53, 3336-3346
-
(2014)
Biochemistry
, vol.53
, pp. 3336-3346
-
-
Arafet, K.1
-
99
-
-
84897401144
-
Differences in conformational dynamics between Plasmodium falciparum and human Hsp90 orthologues enable the structure-based discovery of pathogen-selective inhibitors
-
Wang, T. et al. (2014) Differences in conformational dynamics between Plasmodium falciparum and human Hsp90 orthologues enable the structure-based discovery of pathogen-selective inhibitors. J. Med. Chem. 57, 2524-2535
-
(2014)
J. Med. Chem.
, vol.57
, pp. 2524-2535
-
-
Wang, T.1
-
100
-
-
79959275847
-
How does a drug molecule find its target binding site?
-
Shan, Y. et al. (2011) How does a drug molecule find its target binding site? J. Am. Chem. Soc. 133, 9181-9183
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 9181-9183
-
-
Shan, Y.1
-
101
-
-
79960007037
-
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
-
Buch, I. et al. (2011) Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. Proc. Natl. Acad. Sci. U. S. A. 108, 10184-10189
-
(2011)
Proc. Natl. Acad. Sci. U. S. A.
, vol.108
, pp. 10184-10189
-
-
Buch, I.1
-
102
-
-
1242338103
-
Conformational sampling for the impatient
-
Tai, K. (2004) Conformational sampling for the impatient. Biophys. Chem. 107, 213-220
-
(2004)
Biophys. Chem.
, vol.107
, pp. 213-220
-
-
Tai, K.1
-
103
-
-
0035815288
-
Dynamic coupling between the SH2 and SH3 domains of c-Src and hck underlies their inactivation by C-terminal tyrosine phosphorylation
-
Young, M. A. et al. (2001) Dynamic coupling between the SH2 and SH3 domains of c-Src and hck underlies their inactivation by C-terminal tyrosine phosphorylation. Cell 105, 115-126
-
(2001)
Cell
, vol.105
, pp. 115-126
-
-
Young, M.A.1
-
104
-
-
0002174423
-
Steered molecular dynamics
-
Deuflhard, P. et al. eds, Springer
-
Izrailev, S. et al. (1999) Steered molecular dynamics. In Computational Molecular Dynamics: Challenges, Methods, Ideas (Vol. 4) (Deuflhard, P. et al. eds), pp. 39-65, Springer
-
(1999)
Computational Molecular Dynamics: Challenges, Methods, Ideas
, vol.4
, pp. 39-65
-
-
Izrailev, S.1
-
105
-
-
3142716857
-
Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
-
Hamelberg, D. et al. (2004) Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. J. Chem. Phys. 120, 11919-11929
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 11919-11929
-
-
Hamelberg, D.1
-
106
-
-
0028710015
-
Local elevation - A method for improving the searching properties of molecular-dynamics simulation
-
Huber, T. et al. (1994) Local elevation - a method for improving the searching properties of molecular-dynamics simulation. J. Comput. Aided Mol. Des. 8, 695-708
-
(1994)
J. Comput. Aided Mol. Des.
, vol.8
, pp. 695-708
-
-
Huber, T.1
-
108
-
-
84872255034
-
Computational tools for in silico fragment-based drug design
-
Mortier, J. et al. (2012) Computational tools for in silico fragment-based drug design. Curr. Top. Med. Chem. 12, 1935-1943
-
(2012)
Curr. Top. Med. Chem.
, vol.12
, pp. 1935-1943
-
-
Mortier, J.1
-
110
-
-
0023598484
-
Calculations of electrostatic properties in proteins. Analysis of contributions from induced protein dipoles
-
Van Belle, D. et al. (1987) Calculations of electrostatic properties in proteins. Analysis of contributions from induced protein dipoles. J. Mol. Biol. 198, 721-735
-
(1987)
J. Mol. Biol.
, vol.198
, pp. 721-735
-
-
Van Belle, D.1
-
111
-
-
33748481964
-
Charge equilibration for moleculardynamics simulations
-
Rappe, A. K. and Goddard, W. A. (1991) Charge equilibration for moleculardynamics simulations. J. Phys. Chem. 95, 3358-3363
-
(1991)
J. Phys. Chem.
, vol.95
, pp. 3358-3363
-
-
Rappe, A.K.1
Goddard, W.A.2
-
114
-
-
0001155315
-
Molecular dynamics simulations with interaction potentials including polarization development of a noniterative method and application to water
-
Straatsma, T. P. and McCammon, J. A. (1990) Molecular dynamics simulations with interaction potentials including polarization development of a noniterative method and application to water. Mol. Simul. 5, 181-192
-
(1990)
Mol. Simul.
, vol.5
, pp. 181-192
-
-
Straatsma, T.P.1
McCammon, J.A.2
-
115
-
-
84884194561
-
Polarizable atomic multipole-based AMOEBA force field for proteins
-
Shi, Y. et al. (2013) Polarizable atomic multipole-based AMOEBA force field for proteins. J. Chem. Theory Comput. 9, 4046-4063
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 4046-4063
-
-
Shi, Y.1
-
116
-
-
0347655649
-
CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations
-
Patel, S. and Brooks, C. L. (2004) CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations. J. Comput. Chem. 25, 1-15
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1-15
-
-
Patel, S.1
Brooks, C.L.2
-
117
-
-
84890447773
-
Polarizable force field for peptides and proteins based on the classical Drude oscillator
-
Lopes, P. E. M. et al. (2013) Polarizable force field for peptides and proteins based on the classical Drude oscillator. J. Chem. Theory Comput. 9, 5430-5449
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 5430-5449
-
-
Lopes, P.E.M.1
|