-
1
-
-
84879371161
-
Small-molecule ligand docking into comparative models with Rosetta
-
Combs, S.A. et al. (2013) Small-molecule ligand docking into comparative models with Rosetta. Nat. Protoc., 8, 1277-1298.
-
(2013)
Nat. Protoc.
, vol.8
, pp. 1277-1298
-
-
Combs, S.A.1
-
3
-
-
84918520086
-
Analysis of subpocket selectivity and identification of potent selective inhibitors for matriptase and matriptase-2
-
Duchêne, D. et al. (2014) Analysis of subpocket selectivity and identification of potent selective inhibitors for matriptase and matriptase-2. J. Med. Chem., 57, 10198-10204.
-
(2014)
J. Med. Chem.
, vol.57
, pp. 10198-10204
-
-
Duchêne, D.1
-
4
-
-
84938150763
-
FlexAID: Revisiting docking on non-native-complex structures
-
Gaudreault, F. and Najmanovich, R.J. (2015) FlexAID: revisiting docking on non-native-complex structures. J. Chem. Inf. Model., 55, 1323-1336.
-
(2015)
J. Chem. Inf. Model.
, vol.55
, pp. 1323-1336
-
-
Gaudreault, F.1
Najmanovich, R.J.2
-
5
-
-
30144442036
-
A method for localizing ligand binding pockets in protein structures
-
Glaser, F. et al. (2006) A method for localizing ligand binding pockets in protein structures. Proteins, 62, 479-488.
-
(2006)
Proteins
, vol.62
, pp. 479-488
-
-
Glaser, F.1
-
6
-
-
79960029361
-
SwissDock, a protein-small molecule docking web service based on EADock DSS
-
Grosdidier, A. et al. (2011) SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic Acids Res., 39, W270-W277.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. W270-W277
-
-
Grosdidier, A.1
-
7
-
-
77957898063
-
Scoring functions and their evaluation methods for protein-ligand docking: Recent advances and future directions
-
Huang, S.-Y. et al. (2010) Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions. Phys. Chem. Chem. Phys., 12, 12899-12908.
-
(2010)
Phys. Chem. Chem. Phys.
, vol.12
, pp. 12899-12908
-
-
Huang, S.-Y.1
-
8
-
-
70349211752
-
Automated docking screens: A feasibility study
-
Irwin, J.J. et al. (2009) Automated docking screens: a feasibility study. J. Med. Chem., 52, 5712-5720.
-
(2009)
J. Med. Chem.
, vol.52
, pp. 5712-5720
-
-
Irwin, J.J.1
-
9
-
-
33947420139
-
Shape variation in protein binding pockets and their ligands
-
Kahraman, A. et al. (2007) Shape variation in protein binding pockets and their ligands. J. Mol. Biol., 368, 283-301.
-
(2007)
J. Mol. Biol.
, vol.368
, pp. 283-301
-
-
Kahraman, A.1
-
10
-
-
0033388757
-
Ligand docking and screening with FlexX
-
Kramer, B. et al. (1999) Ligand docking and screening with FlexX. Med. Chem. Res., 9, 463-478.
-
(1999)
Med. Chem. Res.
, vol.9
, pp. 463-478
-
-
Kramer, B.1
-
11
-
-
0028881975
-
Surfnet-A program for visualizing molecular-surfaces, cavities, and intermolecular interactions
-
Laskowski, R. (1995) Surfnet-a program for visualizing molecular-surfaces, cavities, and intermolecular interactions. J. Mol. Graph., 13, 323-330.
-
(1995)
J. Mol. Graph.
, vol.13
, pp. 323-330
-
-
Laskowski, R.1
-
12
-
-
0030447531
-
Protein clefts in molecular recognition and function
-
Laskowski, R.A. et al. (1996) Protein clefts in molecular recognition and function. Protein Sci., 5, 2438-2452.
-
(1996)
Protein Sci.
, vol.5
, pp. 2438-2452
-
-
Laskowski, R.A.1
-
13
-
-
84894639153
-
Istar: A web platform for large-scale protein-ligand docking
-
Li, H. et al. (2014) istar: a web platform for large-scale protein-ligand docking. PLoS ONE, 9, e85678.
-
(2014)
PLoS ONE
, vol.9
, pp. e85678
-
-
Li, H.1
-
14
-
-
78651235334
-
Computer-aided drug design platform using PyMOL
-
Lill, M.A. and Danielson, M.L. (2011) Computer-aided drug design platform using PyMOL. J. Comput. Aided Mol. Des., 25, 13-19.
-
(2011)
J. Comput. Aided Mol. Des.
, vol.25
, pp. 13-19
-
-
Lill, M.A.1
Danielson, M.L.2
-
15
-
-
84902300574
-
KVFinder: Steered identification of protein cavities as a PyMOL plugin
-
Oliveira, S.H. et al. (2014) KVFinder: steered identification of protein cavities as a PyMOL plugin. BMC Bioinformatics, 15, 197.
-
(2014)
BMC Bioinformatics
, vol.15
, pp. 197
-
-
Oliveira, S.H.1
-
16
-
-
84901363730
-
RDock: A fast, versatile and open source program for docking ligands to proteins and nucleic acids
-
Ruiz-Carmona, S. et al. (2014) rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids. PLoS Comput. Biol., 10, e1003571.
-
(2014)
PLoS Comput. Biol.
, vol.10
, pp. e1003571
-
-
Ruiz-Carmona, S.1
-
17
-
-
77953325845
-
Ligand docking and binding site analysis with PyMOL and Autodock/Vina
-
Seeliger, D. and de Groot, B.L. (2010) Ligand docking and binding site analysis with PyMOL and Autodock/Vina. J. Comput. Aided Mol. Des., 24, 417-422.
-
(2010)
J. Comput. Aided Mol. Des.
, vol.24
, pp. 417-422
-
-
Seeliger, D.1
De Groot, B.L.2
-
18
-
-
76149120388
-
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
-
Trott, O. and Olson, A.J. (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem., 31, 455-461.
-
(2010)
J. Comput. Chem.
, vol.31
, pp. 455-461
-
-
Trott, O.1
Olson, A.J.2
-
19
-
-
0038174853
-
Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening
-
Zavodszky, M. et al. (2002) Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening. J. Comput. Aided Mol. Des., 16, 883-902.
-
(2002)
J. Comput. Aided Mol. Des.
, vol.16
, pp. 883-902
-
-
Zavodszky, M.1
|