-
1
-
-
78650727351
-
Conformations and 3D pharmacophore searching
-
Schwab, C. H. Conformations and 3D pharmacophore searching Drug Discovery Today: Technol. 2010, 7, e245-e253 10.1016/j.ddtec.2010.10.003
-
(2010)
Drug Discovery Today: Technol.
, vol.7
, pp. e245-e253
-
-
Schwab, C.H.1
-
2
-
-
0020491251
-
A geometric approach to macromolecule-ligand interactions
-
Kuntz, I. D.; Blaney, J. M.; Oatley, S. J.; Langridge, R.; Ferrin, T. E. A geometric approach to macromolecule-ligand interactions J. Mol. Biol. 1982, 161, 269-288 10.1016/0022-2836(82)90153-X
-
(1982)
J. Mol. Biol.
, vol.161
, pp. 269-288
-
-
Kuntz, I.D.1
Blaney, J.M.2
Oatley, S.J.3
Langridge, R.4
Ferrin, T.E.5
-
3
-
-
0031552362
-
Development and validation of a genetic algorithm for flexible docking
-
Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking J. Mol. Biol. 1997, 267, 727-748 10.1006/jmbi.1996.0897
-
(1997)
J. Mol. Biol.
, vol.267
, pp. 727-748
-
-
Jones, G.1
Willett, P.2
Glen, R.C.3
Leach, A.R.4
Taylor, R.5
-
4
-
-
11644261806
-
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
-
Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function J. Comput. Chem. 1998, 19, 1639-1662 10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B
-
(1998)
J. Comput. Chem.
, vol.19
, pp. 1639-1662
-
-
Morris, G.M.1
Goodsell, D.S.2
Halliday, R.S.3
Huey, R.4
Hart, W.E.5
Belew, R.K.6
Olson, A.J.7
-
5
-
-
77952754227
-
ParaDockS: A framework for molecular docking with population-based metaheuristics
-
Meier, R.; Pippel, M.; Brandt, F.; Sippl, W.; Baldauf, C. ParaDockS: a framework for molecular docking with population-based metaheuristics J. Chem. Inf. Model. 2010, 50, 879-889 10.1021/ci900467x
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 879-889
-
-
Meier, R.1
Pippel, M.2
Brandt, F.3
Sippl, W.4
Baldauf, C.5
-
6
-
-
18344383893
-
Comparison of conformational analysis techniques to generate pharmacophore hypotheses using catalyst
-
Kristam, R.; Gillet, V. J.; Lewis, R. A.; Thorner, D. Comparison of conformational analysis techniques to generate pharmacophore hypotheses using catalyst J. Chem. Inf. Model. 2005, 45, 461-476 10.1021/ci049731z
-
(2005)
J. Chem. Inf. Model.
, vol.45
, pp. 461-476
-
-
Kristam, R.1
Gillet, V.J.2
Lewis, R.A.3
Thorner, D.4
-
7
-
-
18344382014
-
Comparative analysis of protein-bound ligand conformations with respect to catalyst's conformational space subsampling algorithms
-
Kirchmair, J.; Laggner, C.; Wolber, G.; Langer, T. Comparative analysis of protein-bound ligand conformations with respect to catalyst's conformational space subsampling algorithms J. Chem. Inf. Model. 2005, 45, 422-430 10.1021/ci049753l
-
(2005)
J. Chem. Inf. Model.
, vol.45
, pp. 422-430
-
-
Kirchmair, J.1
Laggner, C.2
Wolber, G.3
Langer, T.4
-
8
-
-
34250839505
-
Conformational sampling of bioactive molecules: A comparative study
-
Agrafiotis, D. K.; Gibbs, A. C.; Zhu, F.; Izrailev, S.; Martin, E. Conformational sampling of bioactive molecules: a comparative study J. Chem. Inf. Model. 2007, 47, 1067-1086 10.1021/ci6005454
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 1067-1086
-
-
Agrafiotis, D.K.1
Gibbs, A.C.2
Zhu, F.3
Izrailev, S.4
Martin, E.5
-
9
-
-
35248863951
-
CAESAR: A new conformer generation algorithm based on recursive buildup and local rotational symmetry consideration
-
Li, J.; Ehlers, T.; Sutter, J.; Varma-O'Brien, S.; Kirchmair, J. CAESAR: a new conformer generation algorithm based on recursive buildup and local rotational symmetry consideration J. Chem. Inf. Model. 2007, 47, 1923-1932 10.1021/ci700136x
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 1923-1932
-
-
Li, J.1
Ehlers, T.2
Sutter, J.3
Varma-O'Brien, S.4
Kirchmair, J.5
-
10
-
-
80053512597
-
Open Babel: An open chemical toolbox
-
O'Boyle, N. M.; Banck, M.; James, C. A.; Morley, C.; Vandermeersch, T.; Hutchison, G. R. Open Babel: An open chemical toolbox J. Cheminf. 2011, 3, 33 10.1186/1758-2946-3-33
-
(2011)
J. Cheminf.
, vol.3
, pp. 33
-
-
O'Boyle, N.M.1
Banck, M.2
James, C.A.3
Morley, C.4
Vandermeersch, T.5
Hutchison, G.R.6
-
11
-
-
79954537632
-
Confab - Systematic generation of diverse low-energy conformers
-
O'Boyle, N. M.; Vandermeersch, T.; Flynn, C. J.; Maguire, A. R.; Hutchison, G. R. Confab-Systematic generation of diverse low-energy conformers J. Cheminf. 2011, 3, 8 10.1186/1758-2946-3-8
-
(2011)
J. Cheminf.
, vol.3
, pp. 8
-
-
O'Boyle, N.M.1
Vandermeersch, T.2
Flynn, C.J.3
Maguire, A.R.4
Hutchison, G.R.5
-
12
-
-
84986437005
-
Macromodel - An integrated software system for modeling organic and bioorganic molecules using molecular mechanics
-
Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. Macromodel-An integrated software system for modeling organic and bioorganic molecules using molecular mechanics J. Comput. Chem. 1990, 11, 440-467 10.1002/jcc.540110405
-
(1990)
J. Comput. Chem.
, vol.11
, pp. 440-467
-
-
Mohamadi, F.1
Richards, N.G.J.2
Guida, W.C.3
Liskamp, R.4
Lipton, M.5
Caufield, C.6
Chang, G.7
Hendrickson, T.8
Still, W.C.9
-
13
-
-
0342645331
-
-
Chemical Computing Group, Inc. Montreal, Canada.
-
MOE (Molecular Operating Environment); Chemical Computing Group, Inc.: Montreal, Canada, 2008.
-
(2008)
MOE (Molecular Operating Environment)
-
-
-
14
-
-
84893393300
-
ALFA: Automatic Ligand Flexibility Assignment
-
Klett, J.; Cortés-Cabrera, A.; Gil-Redondo, R.; Gago, F.; Morreale, A. ALFA: Automatic Ligand Flexibility Assignment J. Chem. Inf. Model. 2014, 54, 314-323 10.1021/ci400453n
-
(2014)
J. Chem. Inf. Model.
, vol.54
, pp. 314-323
-
-
Klett, J.1
Cortés-Cabrera, A.2
Gil-Redondo, R.3
Gago, F.4
Morreale, A.5
-
15
-
-
84884985535
-
CONFECT: Conformations from an Expert Collection of Torsion Patterns
-
Schärfer, C.; Schulz-Gasch, T.; Hert, J.; Heinzerling, L.; Schulz, B.; Inhester, T.; Stahl, M.; Rarey, M. CONFECT: Conformations from an Expert Collection of Torsion Patterns ChemMedChem 2013, 1690-1700 10.1002/cmdc.201300242
-
(2013)
ChemMedChem
, pp. 1690-1700
-
-
Schärfer, C.1
Schulz-Gasch, T.2
Hert, J.3
Heinzerling, L.4
Schulz, B.5
Inhester, T.6
Stahl, M.7
Rarey, M.8
-
16
-
-
0028466540
-
Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures
-
Sadowski, J.; Gasteiger, J.; Klebe, G. Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures J. Chem. Inf. Model. 1994, 34, 1000-1008 10.1021/ci00020a039
-
(1994)
J. Chem. Inf. Model.
, vol.34
, pp. 1000-1008
-
-
Sadowski, J.1
Gasteiger, J.2
Klebe, G.3
-
17
-
-
33750434190
-
Impact of conformational flexibility on three-dimensional similarity searching using correlation vectors
-
Renner, S.; Schwab, C. H.; Gasteiger, J.; Schneider, G. Impact of conformational flexibility on three-dimensional similarity searching using correlation vectors J. Chem. Inf. Model. 2006, 46, 2324-2332 10.1021/ci050075s
-
(2006)
J. Chem. Inf. Model.
, vol.46
, pp. 2324-2332
-
-
Renner, S.1
Schwab, C.H.2
Gasteiger, J.3
Schneider, G.4
-
18
-
-
79955389305
-
Data-driven high-throughput prediction of the 3-D structure of small molecules: Review and progress
-
Andronico, A.; Randall, A.; Benz, R. W.; Baldi, P. Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress J. Chem. Inf. Model. 2011, 51, 760-776 10.1021/ci100223t
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 760-776
-
-
Andronico, A.1
Randall, A.2
Benz, R.W.3
Baldi, P.4
-
19
-
-
84896516144
-
Small-molecule 3D structure prediction using open crystallography data
-
Sadowski, P.; Baldi, P. Small-molecule 3D structure prediction using open crystallography data J. Chem. Inf. Model. 2013, 53, 3127-3130 10.1021/ci4005282
-
(2013)
J. Chem. Inf. Model.
, vol.53
, pp. 3127-3130
-
-
Sadowski, P.1
Baldi, P.2
-
20
-
-
77951986384
-
Conformer generation with OMEGA: Algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database
-
Hawkins, P. C. D.; Skillman, A. G.; Warren, G. L.; Ellingson, B. A.; Stahl, M. T. Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database J. Chem. Inf. Model. 2010, 50, 572-584 10.1021/ci100031x
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 572-584
-
-
Hawkins, P.C.D.1
Skillman, A.G.2
Warren, G.L.3
Ellingson, B.A.4
Stahl, M.T.5
-
21
-
-
37249065124
-
Generating conformer ensembles using a multiobjective genetic algorithm
-
Vainio, M. J.; Johnson, M. S. Generating conformer ensembles using a multiobjective genetic algorithm J. Chem. Inf. Model. 2007, 47, 2462-2474 10.1021/ci6005646
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 2462-2474
-
-
Vainio, M.J.1
Johnson, M.S.2
-
22
-
-
65549133951
-
Cyndi: A multi-objective evolution algorithm based method for bioactive molecular conformational generation
-
Liu, X.; Bai, F.; Ouyang, S.; Wang, X.; Li, H.; Jiang, H. Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation BMC Bioinf. 2009, 10, 101 10.1186/1471-2105-10-101
-
(2009)
BMC Bioinf.
, vol.10
, pp. 101
-
-
Liu, X.1
Bai, F.2
Ouyang, S.3
Wang, X.4
Li, H.5
Jiang, H.6
-
23
-
-
0000560869
-
Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms
-
Wales, D. J.; Doye, J. P. K. Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms J. Phys. Chem. A 1997, 101, 5111-5116 10.1021/jp970984n
-
(1997)
J. Phys. Chem. A
, vol.101
, pp. 5111-5116
-
-
Wales, D.J.1
Doye, J.P.K.2
-
24
-
-
2942692078
-
Minima hopping: An efficient search method for the global minimum of the potential energy surface of complex molecular systems
-
Goedecker, S. Minima hopping: an efficient search method for the global minimum of the potential energy surface of complex molecular systems J. Chem. Phys. 2004, 120, 9911-9917 10.1063/1.1724816
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 9911-9917
-
-
Goedecker, S.1
-
25
-
-
0036572216
-
An object-oriented scripting interface to a legacy electronic structure code
-
Bahn, S.; Jacobsen, K. An object-oriented scripting interface to a legacy electronic structure code Comput. Sci. Eng. 2002, 4, 56-66 10.1109/5992.998641
-
(2002)
Comput. Sci. Eng.
, vol.4
, pp. 56-66
-
-
Bahn, S.1
Jacobsen, K.2
-
26
-
-
84947981019
-
-
GMIN: A program for finding global minima and calculating thermodynamic properties from basin-sampling.
-
Wales, D. J. GMIN: A program for finding global minima and calculating thermodynamic properties from basin-sampling. http://www-wales.ch.cam.ac.uk/GMIN/.
-
-
-
Wales, D.J.1
-
27
-
-
84947981020
-
-
Tinker - Software Tools for Molecular Design.
-
Ponder, J. W. Tinker-Software Tools for Molecular Design. http://dasher.wustl.edu/tinker/.
-
-
-
Ponder, J.W.1
-
31
-
-
0030203970
-
Evolutionary algorithms in computer-aided molecular design
-
Clark, D. E.; Westhead, D. R. Evolutionary algorithms in computer-aided molecular design J. Comput.-Aided Mol. Des. 1996, 10, 337-358 10.1007/BF00124503
-
(1996)
J. Comput.-Aided Mol. Des.
, vol.10
, pp. 337-358
-
-
Clark, D.E.1
Westhead, D.R.2
-
33
-
-
0033610078
-
Global optimization of clusters, crystals, and biomolecules
-
Wales, D. J.; Scheraga, H. A. Global optimization of clusters, crystals, and biomolecules Science 1999, 285, 1368-1372 10.1126/science.285.5432.1368
-
(1999)
Science
, vol.285
, pp. 1368-1372
-
-
Wales, D.J.1
Scheraga, H.A.2
-
35
-
-
0032025802
-
Genetic Algorithms in Conformational Analysis
-
Nair, N.; Goodman, J. M. Genetic Algorithms in Conformational Analysis J. Chem. Inf. Model. 1998, 38, 317-320 10.1021/ci970433u
-
(1998)
J. Chem. Inf. Model.
, vol.38
, pp. 317-320
-
-
Nair, N.1
Goodman, J.M.2
-
36
-
-
2442452698
-
+
-
+ Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 7215-7222 10.1073/pnas.0401659101
-
(2004)
Proc. Natl. Acad. Sci. U. S. A.
, vol.101
, pp. 7215-7222
-
-
Damsbo, M.1
Kinnear, B.S.2
Hartings, M.R.3
Ruhoff, P.T.4
Jarrold, M.F.5
Ratner, M.A.6
-
37
-
-
79551616150
-
Design of optimally switchable molecules by genetic algorithms
-
Carstensen, N. O.; Dieterich, J. M.; Hartke, B. Design of optimally switchable molecules by genetic algorithms Phys. Chem. Chem. Phys. 2011, 13, 2903-2910 10.1039/C0CP01065K
-
(2011)
Phys. Chem. Chem. Phys.
, vol.13
, pp. 2903-2910
-
-
Carstensen, N.O.1
Dieterich, J.M.2
Hartke, B.3
-
38
-
-
84857825285
-
Heuristic approaches to the optimization of acceptor systems in bulk heterojunction cells: A computational study
-
Carlotto, S.; Orian, L.; Polimeno, A. Heuristic approaches to the optimization of acceptor systems in bulk heterojunction cells: a computational study Theor. Chem. Acc. 2012, 131, 1191 10.1007/s00214-012-1191-1
-
(2012)
Theor. Chem. Acc.
, vol.131
, pp. 1191
-
-
Carlotto, S.1
Orian, L.2
Polimeno, A.3
-
39
-
-
0012582438
-
Global geometry optimization of clusters using genetic algorithms
-
Hartke, B. Global geometry optimization of clusters using genetic algorithms J. Phys. Chem. 1993, 97, 9973-9976 10.1021/j100141a013
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 9973-9976
-
-
Hartke, B.1
-
40
-
-
0001489865
-
Molecular geometry optimization with a genetic algorithm
-
Deaven, D. M.; Ho, K. M. Molecular geometry optimization with a genetic algorithm Phys. Rev. Lett. 1995, 75, 288-291 10.1103/PhysRevLett.75.288
-
(1995)
Phys. Rev. Lett.
, vol.75
, pp. 288-291
-
-
Deaven, D.M.1
Ho, K.M.2
-
41
-
-
0001603673
-
Global cluster geometry optimization by a phenotype algorithm with Niches: Location of elusive minima, and low-order scaling with cluster size
-
Hartke, B. Global cluster geometry optimization by a phenotype algorithm with Niches: Location of elusive minima, and low-order scaling with cluster size J. Comput. Chem. 1999, 20, 1752-1759 10.1002/(SICI)1096-987X(199912)20:16<1752::AID-JCC7>3.3.CO;2-S
-
(1999)
J. Comput. Chem.
, vol.20
, pp. 1752-1759
-
-
Hartke, B.1
-
42
-
-
1642460094
-
Evolving better nanoparticles: Genetic algorithms for optimizing cluster geometries
-
Johnston, R. L. Evolving better nanoparticles: Genetic algorithms for optimizing cluster geometries Dalt. Trans. 2003, 4193-4207 10.1039/b305686d
-
(2003)
Dalt. Trans.
, pp. 4193-4207
-
-
Johnston, R.L.1
-
43
-
-
29644433519
-
Using genetic algorithms to map first-principles results to model Hamiltonians: Application to the generalized Ising model for alloys
-
Blum, V.; Hart, G. L. W.; Walorski, M. J.; Zunger, A. Using genetic algorithms to map first-principles results to model Hamiltonians: Application to the generalized Ising model for alloys Phys. Rev. B: Condens. Matter Mater. Phys. 2005, 72, 165113 10.1103/PhysRevB.72.165113
-
(2005)
Phys. Rev. B: Condens. Matter Mater. Phys.
, vol.72
, pp. 165113
-
-
Blum, V.1
Hart, G.L.W.2
Walorski, M.J.3
Zunger, A.4
-
44
-
-
65249086250
-
The performance of minima hopping and evolutionary algorithms for cluster structure prediction
-
Schönborn, S. E.; Goedecker, S.; Roy, S.; Oganov, A. R. The performance of minima hopping and evolutionary algorithms for cluster structure prediction J. Chem. Phys. 2009, 130, 144108 10.1063/1.3097197
-
(2009)
J. Chem. Phys.
, vol.130
, pp. 144108
-
-
Schönborn, S.E.1
Goedecker, S.2
Roy, S.3
Oganov, A.R.4
-
45
-
-
78049526746
-
Synergy between theory and experiment in structure resolution of low-dimensional oxides
-
Sierka, M. Synergy between theory and experiment in structure resolution of low-dimensional oxides Prog. Surf. Sci. 2010, 85, 398-434 10.1016/j.progsurf.2010.07.004
-
(2010)
Prog. Surf. Sci.
, vol.85
, pp. 398-434
-
-
Sierka, M.1
-
48
-
-
84881368406
-
Global optimization of clusters using electronic structure methods
-
Heiles, S.; Johnston, R. L. Global optimization of clusters using electronic structure methods Int. J. Quantum Chem. 2013, 113, 2091-2109 10.1002/qua.24462
-
(2013)
Int. J. Quantum Chem.
, vol.113
, pp. 2091-2109
-
-
Heiles, S.1
Johnston, R.L.2
-
49
-
-
17644426018
-
Evolutionary approach for determining first-principles hamiltonians
-
Hart, G. L. W.; Blum, V.; Walorski, M. J.; Zunger, A. Evolutionary approach for determining first-principles hamiltonians Nat. Mater. 2005, 4, 391-394 10.1038/nmat1374
-
(2005)
Nat. Mater.
, vol.4
, pp. 391-394
-
-
Hart, G.L.W.1
Blum, V.2
Walorski, M.J.3
Zunger, A.4
-
50
-
-
33744917515
-
A periodic genetic algorithm with real-space representation for crystal structure and polymorph prediction
-
Abraham, N. L.; Probert, M. I. J. A periodic genetic algorithm with real-space representation for crystal structure and polymorph prediction Phys. Rev. B: Condens. Matter Mater. Phys. 2006, 73, 224104 10.1103/PhysRevB.73.224104
-
(2006)
Phys. Rev. B: Condens. Matter Mater. Phys.
, vol.73
, pp. 224104
-
-
Abraham, N.L.1
Probert, M.I.J.2
-
51
-
-
33745634670
-
Crystal structure prediction using ab initio evolutionary techniques: Principles and applications
-
Oganov, A. R.; Glass, C. W. Crystal structure prediction using ab initio evolutionary techniques: principles and applications J. Chem. Phys. 2006, 124, 244704 10.1063/1.2210932
-
(2006)
J. Chem. Phys.
, vol.124
, pp. 244704
-
-
Oganov, A.R.1
Glass, C.W.2
-
52
-
-
56749159245
-
Crystal structure prediction from first principles
-
Woodley, S. M.; Catlow, R. Crystal structure prediction from first principles Nat. Mater. 2008, 7, 937-946 10.1038/nmat2321
-
(2008)
Nat. Mater.
, vol.7
, pp. 937-946
-
-
Woodley, S.M.1
Catlow, R.2
-
53
-
-
84887594991
-
A grand canonical genetic algorithm for the prediction of multi-component phase diagrams and testing of empirical potentials
-
Tipton, W. W.; Hennig, R. G. A grand canonical genetic algorithm for the prediction of multi-component phase diagrams and testing of empirical potentials J. Phys.: Condens. Matter 2013, 25, 495401 10.1088/0953-8984/25/49/495401
-
(2013)
J. Phys.: Condens. Matter
, vol.25
, pp. 495401
-
-
Tipton, W.W.1
Hennig, R.G.2
-
54
-
-
84859156396
-
Accelerated cluster structure search using electron diffraction data in a genetic algorithm
-
Neiss, C.; Schooss, D. Accelerated cluster structure search using electron diffraction data in a genetic algorithm Chem. Phys. Lett. 2012, 532, 119-123 10.1016/j.cplett.2012.02.062
-
(2012)
Chem. Phys. Lett.
, vol.532
, pp. 119-123
-
-
Neiss, C.1
Schooss, D.2
-
55
-
-
80855139855
-
Optimization of a genetic algorithm for searching molecular conformer space
-
Brain, Z. E.; Addicoat, M. A. Optimization of a genetic algorithm for searching molecular conformer space J. Chem. Phys. 2011, 135, 174106 10.1063/1.3656323
-
(2011)
J. Chem. Phys.
, vol.135
, pp. 174106
-
-
Brain, Z.E.1
Addicoat, M.A.2
-
56
-
-
84882240711
-
How cations change peptide structure
-
Baldauf, C.; Pagel, K.; Warnke, S.; von Helden, G.; Koksch, B.; Blum, V.; Scheffler, M. How cations change peptide structure Chem.-Eur. J. 2013, 19, 11224-11234 10.1002/chem.201204554
-
(2013)
Chem. - Eur. J.
, vol.19
, pp. 11224-11234
-
-
Baldauf, C.1
Pagel, K.2
Warnke, S.3
Von Helden, G.4
Koksch, B.5
Blum, V.6
Scheffler, M.7
-
58
-
-
84945563765
-
Toward Focusing Conformational Ensembles on Bioactive Conformations: A Molecular Mechanics/Quantum Mechanics Study
-
Avgy-David, H. H.; Senderowitz, H. Toward Focusing Conformational Ensembles on Bioactive Conformations: A Molecular Mechanics/Quantum Mechanics Study J. Chem. Inf. Model. 2015, 55, 2154-2167 10.1021/acs.jcim.5b00259
-
(2015)
J. Chem. Inf. Model.
, vol.55
, pp. 2154-2167
-
-
Avgy-David, H.H.1
Senderowitz, H.2
-
59
-
-
0037039459
-
Empirical correction to density functional theory for van der Waals interactions
-
Wu, Q.; Yang, W. Empirical correction to density functional theory for van der Waals interactions J. Chem. Phys. 2002, 116, 515 10.1063/1.1424928
-
(2002)
J. Chem. Phys.
, vol.116
, pp. 515
-
-
Wu, Q.1
Yang, W.2
-
60
-
-
84882394229
-
The accuracy of quantum chemical methods for large noncovalent complexes
-
Sedlak, R.; Janowski, T.; Pitoňák, M.; Řezáč, J.; Pulay, P.; Hobza, P. The accuracy of quantum chemical methods for large noncovalent complexes J. Chem. Theory Comput. 2013, 9, 3364-3374 10.1021/ct400036b
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 3364-3374
-
-
Sedlak, R.1
Janowski, T.2
Pitoňák, M.3
Řezáč, J.4
Pulay, P.5
Hobza, P.6
-
61
-
-
79952713158
-
Unraveling the Stability of Polypeptide Helices: Critical Role of van der Waals Interactions
-
Tkatchenko, A.; Rossi, M.; Blum, V.; Ireta, J.; Scheffler, M. Unraveling the Stability of Polypeptide Helices: Critical Role of van der Waals Interactions Phys. Rev. Lett. 2011, 106, 118102 10.1103/PhysRevLett.106.118102
-
(2011)
Phys. Rev. Lett.
, vol.106
, pp. 118102
-
-
Tkatchenko, A.1
Rossi, M.2
Blum, V.3
Ireta, J.4
Scheffler, M.5
-
62
-
-
33847207462
-
Density functional theory with dispersion corrections for supramolecular structures, aggregates, and complexes of (bio)organic molecules
-
Grimme, S.; Antony, J.; Schwabe, T.; Mück-Lichtenfeld, C. Density functional theory with dispersion corrections for supramolecular structures, aggregates, and complexes of (bio)organic molecules Org. Biomol. Chem. 2007, 5, 741-758 10.1039/b615319b
-
(2007)
Org. Biomol. Chem.
, vol.5
, pp. 741-758
-
-
Grimme, S.1
Antony, J.2
Schwabe, T.3
Mück-Lichtenfeld, C.4
-
63
-
-
77951680464
-
A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu
-
Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu J. Chem. Phys. 2010, 132, 154104 10.1063/1.3382344
-
(2010)
J. Chem. Phys.
, vol.132
, pp. 154104
-
-
Grimme, S.1
Antony, J.2
Ehrlich, S.3
Krieg, H.4
-
64
-
-
61349180195
-
Accurate Molecular Van der Waals Interactions from Ground-State Electron Density and Free-Atom Reference Data
-
Tkatchenko, A.; Scheffler, M. Accurate Molecular Van Der Waals Interactions from Ground-State Electron Density and Free-Atom Reference Data Phys. Rev. Lett. 2009, 102, 073005 10.1103/PhysRevLett.102.073005
-
(2009)
Phys. Rev. Lett.
, vol.102
, pp. 073005
-
-
Tkatchenko, A.1
Scheffler, M.2
-
65
-
-
84861873145
-
Accurate and Efficient Method for Many-Body van der Waals Interactions
-
Tkatchenko, A.; DiStasio, R. A.; Car, R.; Scheffler, M. Accurate and Efficient Method for Many-Body van der Waals Interactions Phys. Rev. Lett. 2012, 108, 236402 10.1103/PhysRevLett.108.236402
-
(2012)
Phys. Rev. Lett.
, vol.108
, pp. 236402
-
-
Tkatchenko, A.1
DiStasio, R.A.2
Car, R.3
Scheffler, M.4
-
66
-
-
84897821292
-
Long-range correlation energy calculated from coupled atomic response functions
-
Ambrosetti, A.; Reilly, A. M.; DiStasio, R. A.; Tkatchenko, A. Long-range correlation energy calculated from coupled atomic response functions J. Chem. Phys. 2014, 140, 18A508 10.1063/1.4865104
-
(2014)
J. Chem. Phys.
, vol.140
, pp. 18A508
-
-
Ambrosetti, A.1
Reilly, A.M.2
DiStasio, R.A.3
Tkatchenko, A.4
-
67
-
-
84924365466
-
+ and the current reach of DFT
-
+ and the current reach of DFT Phys. Chem. Chem. Phys. 2015, 17, 7373 10.1039/C4CP05541A
-
(2015)
Phys. Chem. Chem. Phys.
, vol.17
, pp. 7373
-
-
Schubert, F.1
Rossi, M.2
Baldauf, C.3
Pagel, K.4
Warnke, S.5
Von Helden, G.6
Filsinger, F.7
Kupser, P.8
Meijer, G.9
Salwiczek, M.10
Koksch, B.11
Scheffler, M.12
Blum, V.13
-
68
-
-
70149102016
-
Ab initio molecular simulations with numeric atom-centered orbitals
-
Blum, V.; Gehrke, R.; Hanke, F.; Havu, P.; Havu, V.; Ren, X.; Reuter, K.; Scheffler, M. Ab initio molecular simulations with numeric atom-centered orbitals Comput. Phys. Commun. 2009, 180, 2175-2196 10.1016/j.cpc.2009.06.022
-
(2009)
Comput. Phys. Commun.
, vol.180
, pp. 2175-2196
-
-
Blum, V.1
Gehrke, R.2
Hanke, F.3
Havu, P.4
Havu, V.5
Ren, X.6
Reuter, K.7
Scheffler, M.8
-
69
-
-
70349236830
-
Efficient integration for all-electron electronic structure calculation using numeric basis functions
-
Havu, V.; Blum, V.; Havu, P.; Scheffler, M. Efficient integration for all-electron electronic structure calculation using numeric basis functions J. Comput. Phys. 2009, 228, 8367-8379 10.1016/j.jcp.2009.08.008
-
(2009)
J. Comput. Phys.
, vol.228
, pp. 8367-8379
-
-
Havu, V.1
Blum, V.2
Havu, P.3
Scheffler, M.4
-
70
-
-
0023965741
-
SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules
-
Weininger, D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules J. Chem. Inf. Model. 1988, 28, 31-36 10.1021/ci00057a005
-
(1988)
J. Chem. Inf. Model.
, vol.28
, pp. 31-36
-
-
Weininger, D.1
-
72
-
-
2442583009
-
Structural optimization of atomic clusters by tabu search in descriptor space
-
Cheng, J.; Fournier, R. Structural optimization of atomic clusters by tabu search in descriptor space Theor. Chem. Acc. 2004, 112, 7-15 10.1007/s00214-003-0552-1
-
(2004)
Theor. Chem. Acc.
, vol.112
, pp. 7-15
-
-
Cheng, J.1
Fournier, R.2
-
73
-
-
4243943295
-
Generalized Gradient Approximation Made Simple
-
Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized Gradient Approximation Made Simple Phys. Rev. Lett. 1996, 77, 3865-3868 10.1103/PhysRevLett.77.3865
-
(1996)
Phys. Rev. Lett.
, vol.77
, pp. 3865-3868
-
-
Perdew, J.P.1
Burke, K.2
Ernzerhof, M.3
-
75
-
-
0012189072
-
On the use of a Hessian model function in molecular geometry optimizations
-
Lindh, R.; Bernhardsson, A.; Karlström, G.; Malmqvist, P.-Å. On the use of a Hessian model function in molecular geometry optimizations Chem. Phys. Lett. 1995, 241, 423-428 10.1016/0009-2614(95)00646-L
-
(1995)
Chem. Phys. Lett.
, vol.241
, pp. 423-428
-
-
Lindh, R.1
Bernhardsson, A.2
Karlström, G.3
Malmqvist, P.-A.4
-
76
-
-
84900454935
-
The ELPA library: Scalable parallel eigenvalue solutions for electronic structure theory and computational science
-
Marek, A.; Blum, V.; Johanni, R.; Havu, V.; Lang, B.; Auckenthaler, T.; Heinecke, A.; Bungartz, H.-J.; Lederer, H. The ELPA library: scalable parallel eigenvalue solutions for electronic structure theory and computational science J. Phys.: Condens. Matter 2014, 26, 213201 10.1088/0953-8984/26/21/213201
-
(2014)
J. Phys.: Condens. Matter
, vol.26
, pp. 213201
-
-
Marek, A.1
Blum, V.2
Johanni, R.3
Havu, V.4
Lang, B.5
Auckenthaler, T.6
Heinecke, A.7
Bungartz, H.-J.8
Lederer, H.9
-
77
-
-
77955309392
-
NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations
-
Valiev, M.; Bylaska, E. J.; Govind, N.; Kowalski, K.; Straatsma, T. P.; Van Dam, H. J. J.; Wang, D.; Nieplocha, J.; Apra, E.; Windus, T. L.; de Jong, W. A. NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations Comput. Phys. Commun. 2010, 181, 1477-1489 10.1016/j.cpc.2010.04.018
-
(2010)
Comput. Phys. Commun.
, vol.181
, pp. 1477-1489
-
-
Valiev, M.1
Bylaska, E.J.2
Govind, N.3
Kowalski, K.4
Straatsma, T.P.5
Van Dam, H.J.J.6
Wang, D.7
Nieplocha, J.8
Apra, E.9
Windus, T.L.10
De Jong, W.A.11
-
78
-
-
0037571112
-
Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
-
Halgren, T. A. Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94 J. Comput. Chem. 1996, 17, 490-519 10.1002/(SICI)1096-987X(199604)17:6<490::AID-JCC1>3.3.CO;2-V
-
(1996)
J. Comput. Chem.
, vol.17
, pp. 490-519
-
-
Halgren, T.A.1
-
79
-
-
84905243291
-
Bringing the MMFF force field to the RDKit: Implementation and validation
-
Tosco, P.; Stiefl, N.; Landrum, G. Bringing the MMFF force field to the RDKit: implementation and validation J. Cheminf. 2014, 6, 37 10.1186/s13321-014-0037-3
-
(2014)
J. Cheminf.
, vol.6
, pp. 37
-
-
Tosco, P.1
Stiefl, N.2
Landrum, G.3
-
81
-
-
33847347192
-
Diverse, high-quality test set for the validation of protein-ligand docking performance
-
Hartshorn, M. J.; Verdonk, M. L.; Chessari, G.; Brewerton, S. C.; Mooij, W. T. M.; Mortenson, P. N.; Murray, C. W. Diverse, high-quality test set for the validation of protein-ligand docking performance J. Med. Chem. 2007, 50, 726-41 10.1021/jm061277y
-
(2007)
J. Med. Chem.
, vol.50
, pp. 726-741
-
-
Hartshorn, M.J.1
Verdonk, M.L.2
Chessari, G.3
Brewerton, S.C.4
Mooij, W.T.M.5
Mortenson, P.N.6
Murray, C.W.7
|