-
1
-
-
0027053611
-
A computer graphics method for identifying and displaying protein cavities and their surrounding amino acids
-
Levitt, D.; Banaszak, L. POCKET: A computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. J. Mol. Graphics 1992, 10, 229-243.
-
(1992)
J. Mol. Graphics
, vol.10
, pp. 229-243
-
-
Levitt, D.1
Banaszak2
POCKET, L.3
-
2
-
-
0028881975
-
SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions
-
Laskowski, R. SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J. Mol. Graphics 1995, 13, 323-330.
-
(1995)
J. Mol. Graphics
, vol.13
, pp. 323-330
-
-
Laskowski, R.1
-
3
-
-
0029935202
-
The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria
-
Peters, K. P.; Fauck, J.; Frommel, C. The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria. J. Mol. Biol. 1996, 256, 201-213.
-
(1996)
J. Mol. Biol
, vol.256
, pp. 201-213
-
-
Peters, K.P.1
Fauck, J.2
Frommel, C.3
-
4
-
-
0031370977
-
LIGSITE: Automatic and efficient detection of potential small-molecule binding sites in proteins
-
Hendlich, M.; Rippmann, F.; Barnickel, G. LIGSITE: automatic and efficient detection of potential small-molecule binding sites in proteins. J. Mol. Graphics Modell. 1997, 15, 359-363.
-
(1997)
J. Mol. Graphics Modell
, vol.15
, pp. 359-363
-
-
Hendlich, M.1
Rippmann, F.2
Barnickel, G.3
-
5
-
-
0031687653
-
Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design
-
Liang, J.; Edelsbrunner, H.; Woodward, C. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci. 1998, 7, 1884-1897.
-
(1998)
Protein Sci
, vol.7
, pp. 1884-1897
-
-
Liang, J.1
Edelsbrunner, H.2
Woodward, C.3
-
6
-
-
0342424187
-
Fast prediction and visualization of protein binding pockets with PASS
-
Brady, G. P., Jr.; Stouten, P. F. Fast prediction and visualization of protein binding pockets with PASS. J. Comput.-Aided Mol. Des. 2000, 14, 383-401.
-
(2000)
J. Comput.-Aided Mol. Des
, vol.14
, pp. 383-401
-
-
Brady Jr., G.P.1
Stouten, P.F.2
-
7
-
-
0041989751
-
CASTp: Computed atlas of surface topography of proteins
-
Blinkowski, T.; Naghibzadeh, S.; Liang, J. CASTp: computed atlas of surface topography of proteins. Nucleic Acids Res. 2003, 31, 3352-3355.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3352-3355
-
-
Blinkowski, T.1
Naghibzadeh, S.2
Liang, J.3
-
8
-
-
33750029942
-
CSC: Predicting ligand binding sites using the Connolly surface and degree of conservation
-
accessed June 11, 2007
-
CSC: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct. Biol [Online] 2006, 6. http://www.biomedcentral.com/1472-6807/ 6/ 19 (accessed June 11, 2007).
-
(2006)
BMC Struct. Biol [Online]
, vol.6
-
-
Huang, B.1
Schroeder, M.2
-
9
-
-
21044444449
-
Comprehensive identification and classification of ligand-binding envelopes
-
An, J.; Totrov, M.; Abagyan, R. Comprehensive identification and classification of ligand-binding envelopes. Mol. Cell Proteomics 2005, 4, 752-761.
-
(2005)
Mol. Cell Proteomics
, vol.4
, pp. 752-761
-
-
An, J.1
Totrov, M.2
Abagyan, R.3
-
10
-
-
33646757492
-
On the nature of cavities on protein surfaces: Application to the identification of drug-binding sites
-
Nayal, M.; Honig, B. On the nature of cavities on protein surfaces: application to the identification of drug-binding sites. Proteins 2006, 63, 892-906.
-
(2006)
Proteins
, vol.63
, pp. 892-906
-
-
Nayal, M.1
Honig, B.2
-
11
-
-
0037007068
-
Computational mapping identifies the binding sites of organic solvents on proteins
-
Dennis, S.; Kortvelyesi, T.; Vajda, S. Computational mapping identifies the binding sites of organic solvents on proteins. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 4290-4295.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A
, vol.99
, pp. 4290-4295
-
-
Dennis, S.1
Kortvelyesi, T.2
Vajda, S.3
-
12
-
-
0042856469
-
Improved mapping of protein binding sites
-
Kortvelyesi, T.; Silberstein, M.; Dennis, S.; Vajda, S. Improved mapping of protein binding sites. J. Comput.-Aided Mol. Des. 2003, 17, 173-186.
-
(2003)
J. Comput.-Aided Mol. Des
, vol.17
, pp. 173-186
-
-
Kortvelyesi, T.1
Silberstein, M.2
Dennis, S.3
Vajda, S.4
-
13
-
-
0030979125
-
Automatic identification and representation of protein binding sites for molecular docking
-
Ruppert, J.; Welch, W.; Jain, A. Automatic identification and representation of protein binding sites for molecular docking. Protein Sci. 1997, 6, 524-533.
-
(1997)
Protein Sci
, vol.6
, pp. 524-533
-
-
Ruppert, J.1
Welch, W.2
Jain, A.3
-
14
-
-
0035970295
-
SuperStar: Improved knowledge-based interaction fields for protein binding sites
-
Verdonk, M. L.; Cole, J. C.; Watson, P.; Gillet, V.; Willett, P. SuperStar: improved knowledge-based interaction fields for protein binding sites. J. Mol. Biol. 2001, 307, 841-859, 2001.
-
(2001)
J. Mol. Biol
, vol.2001
, Issue.307
, pp. 841-859
-
-
Verdonk, M.L.1
Cole, J.C.2
Watson, P.3
Gillet, V.4
Willett, P.5
-
15
-
-
0000416633
-
Simple method for locating possible ligand binding sites on protein surfaces
-
Bliznyuk, A.; Gready, J. Simple method for locating possible ligand binding sites on protein surfaces. J. Comput. Chem. 1999, 9, 983-988.
-
(1999)
J. Comput. Chem
, vol.9
, pp. 983-988
-
-
Bliznyuk, A.1
Gready, J.2
-
16
-
-
33846155913
-
Structure-based maximal affinity model predicts small-molecule druggability
-
Cheng, A. C.; Coleman, R. G.; Smyth, K. T.; Cao, Q.; Soulard, P.; Caffrey, D. R.; Salzberg, A. C.; Huang, E. S. Structure-based maximal affinity model predicts small-molecule druggability. Nat. Biotechnol. 2007, 25, 71-75.
-
(2007)
Nat. Biotechnol
, vol.25
, pp. 71-75
-
-
Cheng, A.C.1
Coleman, R.G.2
Smyth, K.T.3
Cao, Q.4
Soulard, P.5
Caffrey, D.R.6
Salzberg, A.C.7
Huang, E.S.8
-
17
-
-
33845806987
-
Structure-based identification of small molecule binding sites using a free-energy model
-
Coleman, R. G.; Salzberg, A.; Cheng, A. C. Structure-based identification of small molecule binding sites using a free-energy model. J. Chem. Inf. Model. 2006, 46, 2631-2637.
-
(2006)
J. Chem. Inf. Model
, vol.46
, pp. 2631-2637
-
-
Coleman, R.G.1
Salzberg, A.2
Cheng, A.C.3
-
18
-
-
11144245309
-
A computational method for the analysis and prediction of protein:phosphopeptide-binding sites
-
Joughin, B. A.; Tidor, B.; Yaffe, M. B. A computational method for the analysis and prediction of protein:phosphopeptide-binding sites. Protein Sci. 2005, 14, 131-139.
-
(2005)
Protein Sci
, vol.14
, pp. 131-139
-
-
Joughin, B.A.1
Tidor, B.2
Yaffe, M.B.3
-
19
-
-
0842274205
-
Rediscovering the sweet spot in drug discovery
-
Brown, D.; Superti-Furga, G. Rediscovering the sweet spot in drug discovery. Drug Discovery Today 2003, 8, 1067-1077.
-
(2003)
Drug Discovery Today
, vol.8
, pp. 1067-1077
-
-
Brown, D.1
Superti-Furga, G.2
-
21
-
-
84868925273
-
-
SiteMap, version 2.2 2008 update release, Schrödinger, LLC: Portland, OR, 2008. Maestro, version 8.5; Schrödinger, LLC: Portland, OR, 2008. QikProp, version 2.5; Schrödinger, LLC: Portland, OR, 2006. OPLS-2001; Schrödinger, LLC: Portland, OR, 2008
-
SiteMap, version 2.2 (2008 update release); Schrödinger, LLC: Portland, OR, 2008. Maestro, version 8.5; Schrödinger, LLC: Portland, OR, 2008. QikProp, version 2.5; Schrödinger, LLC: Portland, OR, 2006. OPLS-2001; Schrödinger, LLC: Portland, OR, 2008.
-
-
-
-
22
-
-
33947420470
-
New method for fast and accurate binding-site identification and analysis
-
Halgren, T. New method for fast and accurate binding-site identification and analysis. Chem. Biol. Drug Des. 2007, 69, 146-148.
-
(2007)
Chem. Biol. Drug Des
, vol.69
, pp. 146-148
-
-
Halgren, T.1
-
23
-
-
20444422149
-
-
Wang, R.; Fang, X.; Lu, Y.; Yang, C.-Y.; Wang, S. The PDBbind database: methodologies and updates. J. Med. Chem. 2005, 48, 4111-4119. PDBbind database, version 2004; University of Michigan: Ann Arbor, MI, 2005.
-
Wang, R.; Fang, X.; Lu, Y.; Yang, C.-Y.; Wang, S. The PDBbind database: methodologies and updates. J. Med. Chem. 2005, 48, 4111-4119. PDBbind database, version 2004; University of Michigan: Ann Arbor, MI, 2005.
-
-
-
-
24
-
-
65249168366
-
-
Wermuth, C. G. The Practice of Medicinal Chemistry, 2nd ed.; Academic Press: London, U.K. and San Diego, CA, 2003.
-
Wermuth, C. G. The Practice of Medicinal Chemistry, 2nd ed.; Academic Press: London, U.K. and San Diego, CA, 2003.
-
-
-
-
25
-
-
24944536065
-
-
Roehrig, S.; Straub, A.; Pohlman, J.; Lampe, T.; Pernerstorfer, J.; Schlemmer, K. H.; Reinemer, P.; Perzborn, E. Discovery of the novel antithrombotic agent 5-chloro-N-({(5S)-2-oxo-3-[4-(3-oxomorpholin-4-yl)phenyl]- 1,3-oxazolidin-5-yl}methyl)thiophene-2-carboxamide (BAY 59-7939): an oral, direct factor Xa inhibitor. J. Med. Chem. 2005, 48, 5900-5908. The crystallographic structure has been solved but does not appear to have been deposited. However, a factor Xa structure with a similar group in the S1 pocket has been deposited as PDB refcode lnfw.
-
Roehrig, S.; Straub, A.; Pohlman, J.; Lampe, T.; Pernerstorfer, J.; Schlemmer, K. H.; Reinemer, P.; Perzborn, E. Discovery of the novel antithrombotic agent 5-chloro-N-({(5S)-2-oxo-3-[4-(3-oxomorpholin-4-yl)phenyl]- 1,3-oxazolidin-5-yl}methyl)thiophene-2-carboxamide (BAY 59-7939): an oral, direct factor Xa inhibitor. J. Med. Chem. 2005, 48, 5900-5908. The crystallographic structure has been solved but does not appear to have been deposited. However, a factor Xa structure with a similar group in the S1 pocket has been deposited as PDB refcode lnfw.
-
-
-
-
26
-
-
35848929515
-
-
Pinto, D. J. P.; Orwat, M. J.; Koch, S.; Rossi, K. A.; Alexander, R. S.; Smallwood, A.; Wong, P. C.; Rendina, A. R.; Luettgen, J. M.; Knabb, R. M.; He, K.; Xin, B.; Wexler, R. R.; Lam, P. Y. Discovery of l-(4-Methoxyphenyl)-7-oxo-6- (4-(2-oxopiperidin-l-yl)phenyl)-4,5,6,7-tet-rahydro-lH-pyrazolo[3,4-c] pyridine-3-carboxamide (Apixaban, BMS-562247), a highly potent, selective, efficacious, and orally bioavailable inhibitor of blood coagulation factor Xa. J. Med. Chem. 2007, 50, 5339-5356. The crystallographic structure is deposited as PDB refcode 2pl6.
-
Pinto, D. J. P.; Orwat, M. J.; Koch, S.; Rossi, K. A.; Alexander, R. S.; Smallwood, A.; Wong, P. C.; Rendina, A. R.; Luettgen, J. M.; Knabb, R. M.; He, K.; Xin, B.; Wexler, R. R.; Lam, P. Y. Discovery of l-(4-Methoxyphenyl)-7-oxo-6- (4-(2-oxopiperidin-l-yl)phenyl)-4,5,6,7-tet-rahydro-lH-pyrazolo[3,4-c] pyridine-3-carboxamide (Apixaban, BMS-562247), a highly potent, selective, efficacious, and orally bioavailable inhibitor of blood coagulation factor Xa. J. Med. Chem. 2007, 50, 5339-5356. The crystallographic structure is deposited as PDB refcode 2pl6.
-
-
-
-
27
-
-
42449113368
-
-
Karlsberg. http://agknapp.chemie.fu-berlin.de/karlsberg (accessed Aug 23, 2008). Kieseritzky, G.; Knapp, E. W. Optimizing pKa computation in proteins with pH adapted conformations. Proteins: Struct., Funct, Bioinf. 2008, 71, 1335-1348.
-
Karlsberg. http://agknapp.chemie.fu-berlin.de/karlsberg (accessed Aug 23, 2008). Kieseritzky, G.; Knapp, E. W. Optimizing pKa computation in proteins with pH adapted conformations. Proteins: Struct., Funct, Bioinf. 2008, 71, 1335-1348.
-
-
-
-
28
-
-
0037434510
-
-
Burgey, C. S, Robinson, K. A, Lyle, T. A, Sanderson, P. E, Lewis, S. D, Lucas, B. J, Krueger, J. A, Singh, R, Miller-Stein, C, White, R. B, Wong, B, Lyle, E. A, Williams, P. D, Coburn, C. A, Dorsey, B. D, Barrow, J. C, Stranieri, M. T, Holahan, M. A, Sitko, G. R, Cook, J. J, McMasters, D. R, McDonough, C. M, Sanders, W. M, Wallace, A. A, Clayton, F. C, Bohn, D, Leonard, Y. M, Detwiler, T. J, Jr, Lynch, J. J, Jr, Yan, Y, Chen, Z, Kuo, L, Gardell, S. J, Shafer, J. A, Vacca, J. P. Metabolism-directed optimization of 3-aminopyrazinone acetamide thrombin inhibitors. Development of an orally bioavailable series containing P1 and P3 pyridines. J. Med. Chem. 2003, 46, 461-473. Crystallographic structures are deposited as PDB refcodes lmu6, lmu8, and lmue
-
Burgey, C. S.; Robinson, K. A.; Lyle, T. A.; Sanderson, P. E.; Lewis, S. D.; Lucas, B. J.; Krueger, J. A.; Singh, R.; Miller-Stein, C.; White, R. B.; Wong, B.; Lyle, E. A.; Williams, P. D.; Coburn, C. A.; Dorsey, B. D.; Barrow, J. C.; Stranieri, M. T.; Holahan, M. A.; Sitko, G. R.; Cook, J. J.; McMasters, D. R.; McDonough, C. M.; Sanders, W. M.; Wallace, A. A.; Clayton, F. C.; Bohn, D.; Leonard, Y. M.; Detwiler, T. J., Jr.; Lynch, J. J., Jr.; Yan, Y.; Chen, Z.; Kuo, L.; Gardell, S. J.; Shafer, J. A.; Vacca, J. P. Metabolism-directed optimization of 3-aminopyrazinone acetamide thrombin inhibitors. Development of an orally bioavailable series containing P1 and P3 pyridines. J. Med. Chem. 2003, 46, 461-473. Crystallographic structures are deposited as PDB refcodes lmu6, lmu8, and lmue.
-
-
-
-
29
-
-
0025925104
-
Design and synthesis of P2-Pl′-linked macrocyclic human renin inhibitors
-
Weber, A.; Halgren, T. A. Design and synthesis of P2-Pl′-linked macrocyclic human renin inhibitors. J. Med. Chem. 1991, 34, 2692-2701.
-
(1991)
J. Med. Chem
, vol.34
, pp. 2692-2701
-
-
Weber, A.1
Halgren, T.A.2
-
30
-
-
0021871375
-
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
-
Goodford, P. J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 1985, 28, 849-857.
-
(1985)
J. Med. Chem
, vol.28
, pp. 849-857
-
-
Goodford, P.J.1
-
31
-
-
12144289984
-
Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
-
Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shaw, D. E.; Shelley, M.; Perry, J. K.; Francis, P.; Shenkin, P. S. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 2004, 47, 1739-1749.
-
(2004)
J. Med. Chem
, vol.47
, pp. 1739-1749
-
-
Friesner, R.A.1
Banks, J.L.2
Murphy, R.B.3
Halgren, T.A.4
Klicic, J.J.5
Mainz, D.T.6
Repasky, M.P.7
Knoll, E.H.8
Shaw, D.E.9
Shelley, M.10
Perry, J.K.11
Francis, P.12
Shenkin, P.S.13
-
32
-
-
1642310340
-
Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening
-
Halgren, T. A.; Murphy, R. B.; Friesner, R. A.; Beard, H. S.; Frye, L. L.; Pollard, W. T.; Banks, J. L. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J. Med. Chem. 2004, 47, 1750-1759.
-
(2004)
J. Med. Chem
, vol.47
, pp. 1750-1759
-
-
Halgren, T.A.1
Murphy, R.B.2
Friesner, R.A.3
Beard, H.S.4
Frye, L.L.5
Pollard, W.T.6
Banks, J.L.7
-
33
-
-
33750124980
-
Extra precision Glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes
-
Friesner, R. A.; Murphy, R. B.; Repasky, M. P.; Frye, L. L.; Greenwood, J. R.; Halgren, T. A.; Sanschagrin, P. C.; Mainz, D. T. Extra precision Glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J. Med. Chem. 2006, 49, 6177-6196.
-
(2006)
J. Med. Chem
, vol.49
, pp. 6177-6196
-
-
Friesner, R.A.1
Murphy, R.B.2
Repasky, M.P.3
Frye, L.L.4
Greenwood, J.R.5
Halgren, T.A.6
Sanschagrin, P.C.7
Mainz, D.T.8
-
34
-
-
0031024171
-
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
-
Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Delivery Rev. 1997, 23, 3-25.
-
(1997)
Adv. Drug Delivery Rev
, vol.23
, pp. 3-25
-
-
Lipinski, C.A.1
Lombardo, F.2
Dominy, B.W.3
Feeney, P.J.4
-
35
-
-
0035438391
-
Is there a difference between leads and drugs? A historical perspective
-
Oprea, T. I.; Davis, A. M.; Teague, S. J.; Leeson, P. D. Is there a difference between leads and drugs? A historical perspective. J. Chem. Inf. Model. 2001, 41, 1308-1315.
-
(2001)
J. Chem. Inf. Model
, vol.41
, pp. 1308-1315
-
-
Oprea, T.I.1
Davis, A.M.2
Teague, S.J.3
Leeson, P.D.4
-
36
-
-
1842790854
-
Synthesis of a novel peptidic photoaffinity probe for the PTP-1B enzyme
-
Therien, M.; Skorey, K.; Zamboni, R.; Li, C. S.; Lau, C. K.; LeRiche, T.; Truong, V. L.; Waddleton, D.; Ramachandran, C. Synthesis of a novel peptidic photoaffinity probe for the PTP-1B enzyme. Bioorg. Med. Chem. Lett. 2004, 14, 2319-2322.
-
(2004)
Bioorg. Med. Chem. Lett
, vol.14
, pp. 2319-2322
-
-
Therien, M.1
Skorey, K.2
Zamboni, R.3
Li, C.S.4
Lau, C.K.5
LeRiche, T.6
Truong, V.L.7
Waddleton, D.8
Ramachandran, C.9
|