-
1
-
-
0041989635
-
Conformational flexibility models for the receptor in structure based drug design
-
This excellent review classifies approaches to the induced fit docking into five categories.
-
Teodoro M.L., and Kavraki L.E. Conformational flexibility models for the receptor in structure based drug design. Curr Pharm Des 9 (2003) 1635-1648. This excellent review classifies approaches to the induced fit docking into five categories.
-
(2003)
Curr Pharm Des
, vol.9
, pp. 1635-1648
-
-
Teodoro, M.L.1
Kavraki, L.E.2
-
2
-
-
0028410583
-
Detailed ab-initio prediction of lysozyme-antibody complex with 1.6-Angstrom accuracy
-
Totrov M., and Abagyan R. Detailed ab-initio prediction of lysozyme-antibody complex with 1.6-Angstrom accuracy. Nat Struct Biol 1 (1994) 259-263
-
(1994)
Nat Struct Biol
, vol.1
, pp. 259-263
-
-
Totrov, M.1
Abagyan, R.2
-
3
-
-
16644366869
-
Molecular modelling prediction of ligand binding site flexibility
-
Yang A.Y.C., Kallblad P., and Mancera R.L. Molecular modelling prediction of ligand binding site flexibility. J Comput Aided Mol Des 18 (2004) 235-250
-
(2004)
J Comput Aided Mol Des
, vol.18
, pp. 235-250
-
-
Yang, A.Y.C.1
Kallblad, P.2
Mancera, R.L.3
-
4
-
-
33750056673
-
ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility
-
Meiler J., and Baker D. ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins 65 (2006) 538-548
-
(2006)
Proteins
, vol.65
, pp. 538-548
-
-
Meiler, J.1
Baker, D.2
-
5
-
-
15244353539
-
Side-chain flexibility in protein-ligand binding: the minimal rotation hypothesis
-
Zavodszky M.I., and Kuhn L.A. Side-chain flexibility in protein-ligand binding: the minimal rotation hypothesis. Protein Sci 14 (2005) 1104-1114
-
(2005)
Protein Sci
, vol.14
, pp. 1104-1114
-
-
Zavodszky, M.I.1
Kuhn, L.A.2
-
6
-
-
0036137713
-
Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock
-
Osterberg F., Morris G.M., Sanner M.F., Olson A.J., and Goodsell D.S. Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins 46 (2002) 34-40
-
(2002)
Proteins
, vol.46
, pp. 34-40
-
-
Osterberg, F.1
Morris, G.M.2
Sanner, M.F.3
Olson, A.J.4
Goodsell, D.S.5
-
7
-
-
1442351132
-
Protein flexibility in ligand docking and virtual screening to protein kinases
-
Cavasotto C.N., and Abagyan R.A. Protein flexibility in ligand docking and virtual screening to protein kinases. J Mol Biol 337 (2004) 209-225
-
(2004)
J Mol Biol
, vol.337
, pp. 209-225
-
-
Cavasotto, C.N.1
Abagyan, R.A.2
-
8
-
-
33847347192
-
Diverse, high-quality test set for the validation of protein-ligand docking performance
-
The Astex team raised important issues concerning potential errors in atomic models of crystallographic structures. They compiled a set of 85 electron-density validated protein ligand complexes that are suitable for benchmarking different docking protocols, including the cross docking ones.
-
Hartshorn M.J., Verdonk M.L., Chessari G., Brewerton S.C., Mooij W.T., Mortenson P.N., and Murray C.W. Diverse, high-quality test set for the validation of protein-ligand docking performance. J Med Chem 50 (2007) 726-741. The Astex team raised important issues concerning potential errors in atomic models of crystallographic structures. They compiled a set of 85 electron-density validated protein ligand complexes that are suitable for benchmarking different docking protocols, including the cross docking ones.
-
(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.5
Mortenson, P.N.6
Murray, C.W.7
-
9
-
-
33644807131
-
Is one solution good enough?
-
discussion 185. The authors highlighted the inherent deficiencies of the current form of the Protein data bank to reflect the conformational flexibility in crystallographic structures. To overcome that obstacle they argue for the NMR-style multiple models.
-
Furnham N., Blundell T.L., DePristo M.A., and Terwilliger T.C. Is one solution good enough?. Nat Struct Mol Biol 13 (2006) 184-185 discussion 185. The authors highlighted the inherent deficiencies of the current form of the Protein data bank to reflect the conformational flexibility in crystallographic structures. To overcome that obstacle they argue for the NMR-style multiple models.
-
(2006)
Nat Struct Mol Biol
, vol.13
, pp. 184-185
-
-
Furnham, N.1
Blundell, T.L.2
DePristo, M.A.3
Terwilliger, T.C.4
-
10
-
-
33747002198
-
Knowledge-based real-space explorations for low-resolution structure determination
-
Furnham N., Dore A.S., Chirgadze D.Y., de Bakker P.I., Depristo M.A., and Blundell T.L. Knowledge-based real-space explorations for low-resolution structure determination. Structure 14 (2006) 1313-1320
-
(2006)
Structure
, vol.14
, pp. 1313-1320
-
-
Furnham, N.1
Dore, A.S.2
Chirgadze, D.Y.3
de Bakker, P.I.4
Depristo, M.A.5
Blundell, T.L.6
-
11
-
-
0038798604
-
Nuclear hormone receptor targeted virtual screening
-
Schapira M., Abagyan R., and Totrov M. Nuclear hormone receptor targeted virtual screening. J Med Chem 46 (2003) 3045-3059
-
(2003)
J Med Chem
, vol.46
, pp. 3045-3059
-
-
Schapira, M.1
Abagyan, R.2
Totrov, M.3
-
12
-
-
0035957528
-
FlexE: efficient molecular docking considering protein structure variations
-
This classical paper offers a way to dock into an ensemble of N structures in such a way that the cumulative time is less than the cumulative time of N docking runs. That is achieved via the unified description of the protein incorporating both fixed and flexible areas.
-
Claussen H., Buning C., Rarey M., and Lengauer T. FlexE: efficient molecular docking considering protein structure variations. J Mol Biol 308 (2001) 377-395. This classical paper offers a way to dock into an ensemble of N structures in such a way that the cumulative time is less than the cumulative time of N docking runs. That is achieved via the unified description of the protein incorporating both fixed and flexible areas.
-
(2001)
J Mol Biol
, vol.308
, pp. 377-395
-
-
Claussen, H.1
Buning, C.2
Rarey, M.3
Lengauer, T.4
-
13
-
-
33746924045
-
Ensemble docking into flexible active sites. Critical evaluation of FlexE against JNK-3 and beta-secretase
-
Polgar T., and Keseru G.M. Ensemble docking into flexible active sites. Critical evaluation of FlexE against JNK-3 and beta-secretase. J Chem Inf Model 46 (2006) 1795-1805
-
(2006)
J Chem Inf Model
, vol.46
, pp. 1795-1805
-
-
Polgar, T.1
Keseru, G.M.2
-
14
-
-
34447550727
-
FLIPDock: docking flexible ligands into flexible receptors
-
A hierarchical and multiresolution description of the pocket structure and flexibility provides a framework for incorporating various types of flexibility into Autodock.
-
Zhao Y., and Sanner M.F. FLIPDock: docking flexible ligands into flexible receptors. Proteins 68 (2007) 726-737. A hierarchical and multiresolution description of the pocket structure and flexibility provides a framework for incorporating various types of flexibility into Autodock.
-
(2007)
Proteins
, vol.68
, pp. 726-737
-
-
Zhao, Y.1
Sanner, M.F.2
-
15
-
-
4744365803
-
Soft docking and multiple receptor conformations in virtual screening
-
The authors made an interesting comparison between the soft repulsion single conformation approach with hard repulsion multiple conformation approach.
-
Ferrari A.M., Wei B.Q.Q., Costantino L., and Shoichet B.K. Soft docking and multiple receptor conformations in virtual screening. J Med Chem 47 (2004) 5076-5084. The authors made an interesting comparison between the soft repulsion single conformation approach with hard repulsion multiple conformation approach.
-
(2004)
J Med Chem
, vol.47
, pp. 5076-5084
-
-
Ferrari, A.M.1
Wei, B.Q.Q.2
Costantino, L.3
Shoichet, B.K.4
-
16
-
-
33846000313
-
Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking
-
Huang S.Y., and Zou X. Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking. Proteins 66 (2007) 399-421
-
(2007)
Proteins
, vol.66
, pp. 399-421
-
-
Huang, S.Y.1
Zou, X.2
-
17
-
-
34247197110
-
Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0
-
Corbeil C.R., Englebienne P., and Moitessier N. Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0. J Chem Inf Model 47 (2007) 435-449
-
(2007)
J Chem Inf Model
, vol.47
, pp. 435-449
-
-
Corbeil, C.R.1
Englebienne, P.2
Moitessier, N.3
-
18
-
-
1842471241
-
Testing a flexible-receptor docking algorithm in a model binding site
-
Wei B.Q., Weaver L.H., Ferrari A.M., Matthews B.W., and Shoichet B.K. Testing a flexible-receptor docking algorithm in a model binding site. J Mol Biol 337 (2004) 1161-1182
-
(2004)
J Mol Biol
, vol.337
, pp. 1161-1182
-
-
Wei, B.Q.1
Weaver, L.H.2
Ferrari, A.M.3
Matthews, B.W.4
Shoichet, B.K.5
-
19
-
-
37349085453
-
A flexible approach to induced fit docking
-
The authors used a combination of FlexX-Ensemble docking with the Yasara/Yamber2 program for conformational generation and full atom refinement of the high-ranking complexes. The 'flexible' residues were pre-selected using a set of rules. The protocol was tested on 20 cross docking ligand-protein pairs.
-
Nabuurs S.B., Wagener M., and de Vlieg J. A flexible approach to induced fit docking. J Med Chem 50 (2007) 6507-6518. The authors used a combination of FlexX-Ensemble docking with the Yasara/Yamber2 program for conformational generation and full atom refinement of the high-ranking complexes. The 'flexible' residues were pre-selected using a set of rules. The protocol was tested on 20 cross docking ligand-protein pairs.
-
(2007)
J Med Chem
, vol.50
, pp. 6507-6518
-
-
Nabuurs, S.B.1
Wagener, M.2
de Vlieg, J.3
-
20
-
-
21244479779
-
Unveiling the full potential of flexible receptor docking using multiple crystallographic structures
-
Barril X., and Morley S.D. Unveiling the full potential of flexible receptor docking using multiple crystallographic structures. J Med Chem 48 (2005) 4432-4443
-
(2005)
J Med Chem
, vol.48
, pp. 4432-4443
-
-
Barril, X.1
Morley, S.D.2
-
21
-
-
33645961330
-
Flexible protein-protein docking
-
This excellent review highlights the induced fit problems and attempts to overcome them in protein-protein docking. The issues and the methods translate well into the ligand protein field.
-
Bonvin A.M. Flexible protein-protein docking. Curr Opin Struct Biol 16 (2006) 194-200. This excellent review highlights the induced fit problems and attempts to overcome them in protein-protein docking. The issues and the methods translate well into the ligand protein field.
-
(2006)
Curr Opin Struct Biol
, vol.16
, pp. 194-200
-
-
Bonvin, A.M.1
-
22
-
-
0036769168
-
Imatinib: a selective tyrosine kinase inhibitor
-
Manley P.W., Cowan-Jacob S.W., Buchdunger E., Fabbro D., Fendrich G., Furet P., Meyer T., and Zimmermann J. Imatinib: a selective tyrosine kinase inhibitor. Eur J Cancer 38 Suppl. 5 (2002) S19-S27
-
(2002)
Eur J Cancer
, vol.38
, Issue.SUPPL. 5
-
-
Manley, P.W.1
Cowan-Jacob, S.W.2
Buchdunger, E.3
Fabbro, D.4
Fendrich, G.5
Furet, P.6
Meyer, T.7
Zimmermann, J.8
-
23
-
-
33846457931
-
Structural biology contributions to the discovery of drugs to treat chronic myelogenous leukaemia
-
The Paul Manley/Sandra Cowan-Jacob team review the structural aspects of the discovery Gleevec and its complexes with kinases. They show how understanding the structure and dynamics of the complex helps to design the next generation of drugs with improved properties.
-
Cowan-Jacob S.W., Fendrich G., Floersheimer A., Furet P., Liebetanz J., Rummel G., Rheinberger P., Centeleghe M., Fabbro D., and Manley P.W. Structural biology contributions to the discovery of drugs to treat chronic myelogenous leukaemia. Acta Crystallogr D Biol Crystallogr 63 (2007) 80-93. The Paul Manley/Sandra Cowan-Jacob team review the structural aspects of the discovery Gleevec and its complexes with kinases. They show how understanding the structure and dynamics of the complex helps to design the next generation of drugs with improved properties.
-
(2007)
Acta Crystallogr D Biol Crystallogr
, vol.63
, pp. 80-93
-
-
Cowan-Jacob, S.W.1
Fendrich, G.2
Floersheimer, A.3
Furet, P.4
Liebetanz, J.5
Rummel, G.6
Rheinberger, P.7
Centeleghe, M.8
Fabbro, D.9
Manley, P.W.10
-
24
-
-
21644473891
-
Representing receptor flexibility in ligand docking through relevant normal modes
-
Cavasotto C.N., Kovacs J.A., and Abagyan R.A. Representing receptor flexibility in ligand docking through relevant normal modes. J Am Chem Soc 127 (2005) 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
-
-
4544310320
-
Modeling correlated main-chain motions in proteins for flexible molecular recognition
-
Zavodszky M.I., Ming L., Thorpe M.F., Day A.R., and Kuhn L.A. Modeling correlated main-chain motions in proteins for flexible molecular recognition. Proteins-Struct Funct Bioinform 57 (2004) 243-261
-
(2004)
Proteins-Struct Funct Bioinform
, vol.57
, pp. 243-261
-
-
Zavodszky, M.I.1
Ming, L.2
Thorpe, M.F.3
Day, A.R.4
Kuhn, L.A.5
-
26
-
-
33744488325
-
Discovering new classes of Brugia malayi asparaginyl-tRNA synthetase inhibitors and relating specificity to conformational change
-
Sukuru S.C.K., Crepin T., Milev Y., Marsh L.C., Hill J.B., Anderson R.J., Morris J.C., Rohatgi A., O'Mahony G., Grotli M., et al. Discovering new classes of Brugia malayi asparaginyl-tRNA synthetase inhibitors and relating specificity to conformational change. J Comput Aided Mol Des 20 (2006) 159-178
-
(2006)
J Comput Aided Mol Des
, vol.20
, pp. 159-178
-
-
Sukuru, S.C.K.1
Crepin, T.2
Milev, Y.3
Marsh, L.C.4
Hill, J.B.5
Anderson, R.J.6
Morris, J.C.7
Rohatgi, A.8
O'Mahony, G.9
Grotli, M.10
-
27
-
-
34447271743
-
Exploring experimental sources of multiple protein conformations in structure-based drug design
-
Damm K.L., and Carlson H.A. Exploring experimental sources of multiple protein conformations in structure-based drug design. J Am Chem Soc 129 (2007) 8225-8235
-
(2007)
J Am Chem Soc
, vol.129
, pp. 8225-8235
-
-
Damm, K.L.1
Carlson, H.A.2
-
28
-
-
26444552906
-
Functional plasticity in the substrate binding site of beta-secretase
-
Gorfe A.A., and Caflisch A. Functional plasticity in the substrate binding site of beta-secretase. Structure 13 (2005) 1487-1498
-
(2005)
Structure
, vol.13
, pp. 1487-1498
-
-
Gorfe, A.A.1
Caflisch, A.2
-
29
-
-
28644443463
-
Molecular docking of balanol to dynamics snapshots of protein kinase A
-
Wong C.F., Kua J., Zhang Y.K., Straatsma T.P., and McCammon J.A. Molecular docking of balanol to dynamics snapshots of protein kinase A. Proteins-Struct Funct Bioinform 61 (2005) 850-858
-
(2005)
Proteins-Struct Funct Bioinform
, vol.61
, pp. 850-858
-
-
Wong, C.F.1
Kua, J.2
Zhang, Y.K.3
Straatsma, T.P.4
McCammon, J.A.5
-
30
-
-
34547522758
-
Discovery of antiandrogen activity of nonsteroidal scaffolds of marketed drugs
-
Bisson W.H., Cheltsov A.V., Bruey-Sedano N., Lin B., Chen J., Goldberger N., May L.T., Christopoulos A., Dalton J.T., Sexton P.M., et al. Discovery of antiandrogen activity of nonsteroidal scaffolds of marketed drugs. Proc Natl Acad Sci USA 104 (2007) 11927-11932
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 11927-11932
-
-
Bisson, W.H.1
Cheltsov, A.V.2
Bruey-Sedano, N.3
Lin, B.4
Chen, J.5
Goldberger, N.6
May, L.T.7
Christopoulos, A.8
Dalton, J.T.9
Sexton, P.M.10
-
31
-
-
0027185404
-
A method to configure protein side-chains from the main-chain trace in homology modeling
-
Eisenmenger F., Argos P., and Abagyan R. A method to configure protein side-chains from the main-chain trace in homology modeling. J Mol Biol 231 (1993) 849-860
-
(1993)
J Mol Biol
, vol.231
, pp. 849-860
-
-
Eisenmenger, F.1
Argos, P.2
Abagyan, R.3
-
32
-
-
31544450787
-
Novel procedure for modeling ligand/receptor induced fit effects
-
Sherman W., Day T., Jacobson M.P., Friesner R.A., and Farid R. Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem 49 (2006) 534-553
-
(2006)
J Med Chem
, vol.49
, pp. 534-553
-
-
Sherman, W.1
Day, T.2
Jacobson, M.P.3
Friesner, R.A.4
Farid, R.5
|