-
1
-
-
84879634846
-
Structure determination of membrane proteins by nuclear magnetic resonance spectroscopy
-
Opella, S. J. (2013) Structure determination of membrane proteins by nuclear magnetic resonance spectroscopy. Annu. Rev. Anal. Chem., 6, 305-328.
-
(2013)
Annu. Rev. Anal. Chem.
, vol.6
, pp. 305-328
-
-
Opella, S.J.1
-
2
-
-
84952639674
-
Crosslinking and mass Spectrometry: An integrated technology to understand the structure and function of molecular machines
-
Leitner, A., Faini, M., Stengel, F. and Aebersold, R. (2016) Crosslinking and mass Spectrometry: An integrated technology to understand the structure and function of molecular machines. Trends Biochem. Sci., 41, 20-32.
-
(2016)
Trends Biochem. Sci.
, vol.41
, pp. 20-32
-
-
Leitner, A.1
Faini, M.2
Stengel, F.3
Aebersold, R.4
-
3
-
-
84898766164
-
Super Spy variants implicate flexibility in chaperone action
-
Quan, S., Wang, L., Petrotchenko, E. V., Makepeace, K. A., Horowitz, S., Yang, J., Zhang, Y., Borchers, C. H. and Bardwell, J. C. (2014) Super Spy variants implicate flexibility in chaperone action. Elife, 3, e01584.
-
(2014)
Elife
, vol.3
, pp. e01584
-
-
Quan, S.1
Wang, L.2
Petrotchenko, E.V.3
Makepeace, K.A.4
Horowitz, S.5
Yang, J.6
Zhang, Y.7
Borchers, C.H.8
Bardwell, J.C.9
-
4
-
-
38349100452
-
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
-
Brylinski, M. and Skolnick, J. (2008) A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc. Natl. Acad. Sci. U. S. A., 105, 129-134.
-
(2008)
Proc. Natl. Acad. Sci. U. S. A.
, vol.105
, pp. 129-134
-
-
Brylinski, M.1
Skolnick, J.2
-
5
-
-
74549149999
-
Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure
-
Capra, J. A., Laskowski, R. A., Thornton, J. M., Singh, M. and Funkhouser, T. A. (2009) Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. PLoS Comput. Biol., 5, e1000585.
-
(2009)
PLoS Comput. Biol.
, vol.5
, pp. e1000585
-
-
Capra, J.A.1
Laskowski, R.A.2
Thornton, J.M.3
Singh, M.4
Funkhouser, T.A.5
-
6
-
-
84864460609
-
COFACTOR: An accurate comparative algorithm for structure-based protein function annotation
-
Roy, A., Yang, J. and Zhang, Y. (2012) COFACTOR: an accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Res., 40, W471-W477.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. W471-W477
-
-
Roy, A.1
Yang, J.2
Zhang, Y.3
-
7
-
-
84885655034
-
Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment
-
Yang, J., Roy, A. and Zhang, Y. (2013) Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics, 29, 2588-2595.
-
(2013)
Bioinformatics
, vol.29
, pp. 2588-2595
-
-
Yang, J.1
Roy, A.2
Zhang, Y.3
-
8
-
-
84904823376
-
GalaxySite: Ligand-binding-site prediction by using molecular docking
-
Heo, L., Shin, W. H., Lee, M. S. and Seok, C. (2014) GalaxySite: ligand-binding-site prediction by using molecular docking. Nucleic Acids Res., 42, W210-W214.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. W210-W214
-
-
Heo, L.1
Shin, W.H.2
Lee, M.S.3
Seok, C.4
-
9
-
-
84883574367
-
The FunFOLD2 server for the prediction of protein-ligand interactions
-
Roche, D. B., Buenavista, M. T. and McGuffin, L. J. (2013) The FunFOLD2 server for the prediction of protein-ligand interactions. Nucleic Acids Res., 41, W303-W307.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. W303-W307
-
-
Roche, D.B.1
Buenavista, M.T.2
McGuffin, L.J.3
-
10
-
-
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
-
11
-
-
33846000313
-
Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking
-
Huang, S. Y. and Zou, X. (2007) Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking. Proteins, 66, 399-421.
-
(2007)
Proteins
, vol.66
, pp. 399-421
-
-
Huang, S.Y.1
Zou, X.2
-
12
-
-
84928550315
-
DOCK 6: Impact of new features and current docking performance
-
Allen, W. J., Balius, T. E., Mukherjee, S., Brozell, S. R., Moustakas, D. T., Lang, P. T., Case, D. A., Kuntz, I. D. and Rizzo, R. C. (2015) DOCK 6: Impact of new features and current docking performance. J. Comput. Chem., 36, 1132-1156.
-
(2015)
J. Comput. Chem.
, vol.36
, pp. 1132-1156
-
-
Allen, W.J.1
Balius, T.E.2
Mukherjee, S.3
Brozell, S.R.4
Moustakas, D.T.5
Lang, P.T.6
Case, D.A.7
Kuntz, I.D.8
Rizzo, R.C.9
-
13
-
-
84871604119
-
GalaxyDock: Protein-ligand docking with flexible protein side-chains
-
Shin, W. H. and Seok, C. (2012) GalaxyDock: protein-ligand docking with flexible protein side-chains. J. Chem. Inf. Model., 52, 3225-3232.
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 3225-3232
-
-
Shin, W.H.1
Seok, C.2
-
14
-
-
85013653033
-
Forging the basis for developing protein-ligand interaction scoring functions
-
Liu, Z., Su, M., Han, L., Liu, J., Yang, Q., Li, Y. and Wang, R. (2017) Forging the basis for developing protein-ligand interaction scoring functions. Acc. Chem. Res., 50, 302-309.
-
(2017)
Acc. Chem. Res.
, vol.50
, pp. 302-309
-
-
Liu, Z.1
Su, M.2
Han, L.3
Liu, J.4
Yang, Q.5
Li, Y.6
Wang, R.7
-
15
-
-
85018596195
-
Structural and sequence similarity makes a significant impact on machine-learning-based scoring functions for protein-ligand interactions
-
Li, Y. and Yang, J. (2017) Structural and sequence similarity makes a significant impact on machine-learning-based scoring functions for protein-ligand interactions. J. Chem. Inf. Model., 57, 1007-1012.
-
(2017)
J. Chem. Inf. Model.
, vol.57
, pp. 1007-1012
-
-
Li, Y.1
Yang, J.2
-
16
-
-
84883481556
-
The protein model Portal-a comprehensive resource for protein structure and model information
-
Haas, J., Roth, S., Arnold, K., Kiefer, F., Schmidt, T., Bordoli, L. and Schwede, T. (2013) The protein model Portal-a comprehensive resource for protein structure and model information. Database, 2013, bat031.
-
(2013)
Database
, vol.2013
, pp. bat031
-
-
Haas, J.1
Roth, S.2
Arnold, K.3
Kiefer, F.4
Schmidt, T.5
Bordoli, L.6
Schwede, T.7
-
17
-
-
84925156346
-
The I-TASSER Suite: Protein structure and function prediction
-
Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J. and Zhang, Y. (2015) The I-TASSER Suite: protein structure and function prediction. Nat. Methods, 12, 7-8.
-
(2015)
Nat. Methods
, vol.12
, pp. 7-8
-
-
Yang, J.1
Yan, R.2
Roy, A.3
Xu, D.4
Poisson, J.5
Zhang, Y.6
-
18
-
-
84876574278
-
BioLiP: A semi-manually curated database for biologically relevant ligand-protein interactions
-
Yang, J., Roy, A. and Zhang, Y. (2013) BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. Nucleic Acids Res., 41, D1096-D1103.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D1096-D1103
-
-
Yang, J.1
Roy, A.2
Zhang, Y.3
-
19
-
-
85016111024
-
The RCSB protein data bank: Integrative view of protein, gene and 3D structural information
-
Rose, P. W., Prlic, A., Altunkaya, A., Bi, C., Bradley, A. R., Christie, C. H., Costanzo, L. D., Duarte, J. M., Dutta, S., Feng, Z. et al. (2017) The RCSB protein data bank: integrative view of protein, gene and 3D structural information. Nucleic Acids Res., 45, D271-D281.
-
(2017)
Nucleic Acids Res.
, vol.45
, pp. D271-D281
-
-
Rose, P.W.1
Prlic, A.2
Altunkaya, A.3
Bi, C.4
Bradley, A.R.5
Christie, C.H.6
Costanzo, L.D.7
Duarte, J.M.8
Dutta, S.9
Feng, Z.10
-
20
-
-
84927720583
-
3Dmol. Js: Molecular visualization with WebGL
-
Rego, N. and Koes, D. (2015) 3Dmol. js: molecular visualization with WebGL. Bioinformatics, 31, 1322-1324.
-
(2015)
Bioinformatics
, vol.31
, pp. 1322-1324
-
-
Rego, N.1
Koes, D.2
-
21
-
-
78149275853
-
The binding site distance test score: A robust method for the assessment of predicted protein binding sites
-
Roche, D. B., Tetchner, S. J. and McGuffin, L. J. (2010) The binding site distance test score: a robust method for the assessment of predicted protein binding sites. Bioinformatics, 26, 2920-2921.
-
(2010)
Bioinformatics
, vol.26
, pp. 2920-2921
-
-
Roche, D.B.1
Tetchner, S.J.2
McGuffin, L.J.3
-
22
-
-
84864448769
-
Template-based protein structure modeling using the RaptorX web server
-
Kallberg, M., Wang, H., Wang, S., Peng, J., Wang, Z., Lu, H. and Xu, J. (2012) Template-based protein structure modeling using the RaptorX web server. Nat. Protoc., 7, 1511-1522.
-
(2012)
Nat. Protoc.
, vol.7
, pp. 1511-1522
-
-
Kallberg, M.1
Wang, H.2
Wang, S.3
Peng, J.4
Wang, Z.5
Lu, H.6
Xu, J.7
|