-
1
-
-
21044444449
-
Pocketome via comprehensive identification and classification of ligand binding envelopes
-
6, 20, 21
-
An J., Totrov M., Abagyan R.: Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol. Cell. Proteomics 4, 6 (2005), 752–761. 6, 20, 21
-
(2005)
Mol. Cell. Proteomics
, vol.4
, Issue.6
, pp. 752-761
-
-
An, J.1
Totrov, M.2
Abagyan, R.3
-
2
-
-
84871936785
-
Software tools for identification, visualization and analysis of protein tunnels and channels
-
1
-
Brezovský J., Chovancová E., Gora A., Pavelka A., Biedermannová L., Damborský J.: Software tools for identification, visualization and analysis of protein tunnels and channels. Biotechnol.Adv. 31, 1 (2013), 38–49. 1
-
(2013)
Biotechnol.Adv.
, vol.31
, Issue.1
, pp. 38-49
-
-
Brezovský, J.1
Chovancová, E.2
Gora, A.3
Pavelka, A.4
Biedermannová, L.5
Damborský, J.6
-
3
-
-
84864486886
-
MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels
-
9
-
Berka K., Hanák O., Sehnal D., Banáš P., Navrátilová V., Jaiswal D., Ionescu C.-M., Svobodová Vařeková R., Koča J., Otyepka M.: MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic Acids Res. 40, W1 (2012), W222–227. 9
-
(2012)
Nucleic Acids Res.
, vol.40
, Issue.W1
, pp. W222-227
-
-
Berka, K.1
Hanák, O.2
Sehnal, D.3
Banáš, P.4
Navrátilová, V.5
Jaiswal, D.6
Ionescu, C.-M.7
Svobodová Vařeková, R.8
Koča, J.9
Otyepka, M.10
-
4
-
-
84937897690
-
MoleCollar and Tunnel Heat Map Visualizations for Conveying spatio-Temporo-Chemical Properties Across and Along Protein Voids
-
17
-
Byška J., Jurčík A., Gröller M. E, Viola I., KOZLÍKOVÁ B.: MoleCollar and Tunnel Heat Map Visualizations for Conveying spatio-Temporo-Chemical Properties Across and Along Protein Voids. Comput. Graph. Forum 34, 3 (2015), 1–10. 17
-
(2015)
Comput. Graph. Forum
, vol.34
, Issue.3
, pp. 1-10
-
-
Byška, J.1
Jurčík, A.2
Gröller, M.E.3
Viola, I.4
Kozlíková, B.5
-
5
-
-
0342424187
-
Fast prediction and visualization of protein binding pockets with PASS
-
12, 14, 21
-
Brady Jr. G. P., Stouten P. F. W.: Fast prediction and visualization of protein binding pockets with PASS. J. Comput. Aided Mol. Des. 14, 4 (2000), 383–401. 12, 14, 21
-
(2000)
J. Comput. Aided Mol. Des.
, vol.14
, Issue.4
, pp. 383-401
-
-
Brady, G.P.1
Stouten, P.F.W.2
-
6
-
-
84946606231
-
AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics
-
17
-
Byška J., Muzic M.L., Gröller M. E, Viola I., Kozlíková B.: AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics. IEEE Trans. Vis. Comput. Graphics 22, 1 (2016), 747–756. 17
-
(2016)
IEEE Trans. Vis. Comput. Graphics
, vol.22
, Issue.1
, pp. 747-756
-
-
Byška, J.1
Muzic, M.L.2
Gröller, M.E.3
Viola, I.4
Kozlíková, B.5
-
7
-
-
79952940425
-
Ambient Occlusion Opacity Mapping for Visualization of Internal Molecular Structure
-
18
-
Borland D.: Ambient Occlusion Opacity Mapping for Visualization of Internal Molecular Structure. Journal of WSCG 19, 1 (2011), 17–24. 18
-
(2011)
Journal of WSCG
, vol.19
, Issue.1
, pp. 17-24
-
-
Borland, D.1
-
8
-
-
0029633168
-
GROMACS: A message-passing parallel molecular dynamics implementation
-
7
-
Berendsen H. J. C., van der Spoel D., van Drunen R.: GROMACS: A message-passing parallel molecular dynamics implementation. Comput. Phys. Commun. 91, 1–3 (1995), 43–56. 7
-
(1995)
Comput. Phys. Commun.
, vol.91
, Issue.1
, pp. 43
-
-
Berendsen, H.J.C.1
van der Spoel, D.2
van Drunen, R.3
-
9
-
-
0033954256
-
The Protein Data Bank
-
15
-
Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E.: The Protein Data Bank. Nucl. Acids Res. 28, 1 (2000), 235–242. 15
-
(2000)
Nucl. Acids Res.
, vol.28
, Issue.1
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
10
-
-
79551679034
-
Encoding Molecular Motions in Voxel Maps
-
10, 19, 21
-
Cortés J., Barbe S., Erard M., Siméon T.: Encoding Molecular Motions in Voxel Maps. IEEE/ACM Trans. Comput. Biol. Bioinformatics 8, 2 (2011), 557–563. 10, 19, 21
-
(2011)
IEEE/ACM Trans. Comput. Biol. Bioinformatics
, vol.8
, Issue.2
, pp. 557-563
-
-
Cortés, J.1
Barbe, S.2
Erard, M.3
Siméon, T.4
-
11
-
-
35948994554
-
Molecular Surface Abstraction
-
18, 19
-
Cipriano G., Gleicher M.: Molecular Surface Abstraction. IEEE Trans. Vis. Comput. Graphics 13, 6 (2007), 1608–1615. 18, 19
-
(2007)
IEEE Trans. Vis. Comput. Graphics
, vol.13
, Issue.6
, pp. 1608-1615
-
-
Cipriano, G.1
Gleicher, M.2
-
12
-
-
74549149999
-
Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3d Structure
-
21
-
Capra J.A., Laskowski R.A., Thornton J.M., Singh M., Funkhouser T.A.: Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3d Structure. PLoS Comput Biol 5, 12 (2009), e1000585. 21
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.12
-
-
Capra, J.A.1
Laskowski, R.A.2
Thornton, J.M.3
Singh, M.4
Funkhouser, T.A.5
-
13
-
-
84868156224
-
CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
-
9, 16, 21
-
Chovancová E., Pavelka A., Beneš P., Strnad O., Brezovský J., Kozlíková B., Gora A., Šustr V., Klvaňa M., Medek P., Biedermannová L., Sochor J., Damborský J.: CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures. PLoS Comput. Biol. 8, 10 (2012), e1002708. 9, 16, 21
-
(2012)
PLoS Comput. Biol.
, vol.8
, Issue.10
-
-
Chovancová, E.1
Pavelka, A.2
Beneš, P.3
Strnad, O.4
Brezovský, J.5
Kozlíková, B.6
Gora, A.7
Šustr, V.8
Klvaňa, M.9
Medek, P.10
Biedermannová, L.11
Sochor, J.12
Damborský, J.13
-
14
-
-
84869874067
-
Local functional descriptors for surface comparison based binding prediction
-
18
-
Cipriano G.M., Phillips G.N., Gleicher M.: Local functional descriptors for surface comparison based binding prediction. BMC Bioinformatics 13 (2012), 314. 18
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 314
-
-
Cipriano, G.M.1
Phillips, G.N.2
Gleicher, M.3
-
15
-
-
77957836353
-
Multi-Scale Surface Descriptors
-
18
-
Cipriano G., Phillips, Jr. G. N, Gleicher M.: Multi-Scale Surface Descriptors. IEEE Trans. Vis. Comput. Graphics 15, 6 (2009), 1201–1208. 18
-
(2009)
IEEE Trans. Vis. Comput. Graphics
, vol.15
, Issue.6
, pp. 1201-1208
-
-
Cipriano, G.1
Phillips, G.N.2
Gleicher, M.3
-
16
-
-
33748102999
-
Travel Depth, a New Shape Descriptor for Macromolecules: Application to Ligand Binding
-
18
-
Coleman R.G., Sharp K.A.: Travel Depth, a New Shape Descriptor for Macromolecules: Application to Ligand Binding. J. Mol. Biol. 362, 3 (2006), 441–458. 18
-
(2006)
J. Mol. Biol.
, vol.362
, Issue.3
, pp. 441-458
-
-
Coleman, R.G.1
Sharp, K.A.2
-
17
-
-
34548133728
-
Predicting functionally important residues from sequence conservation
-
21
-
Capra J.A., Singh M.: Predicting functionally important residues from sequence conservation. Bioinformatics 23, 15 (2007), 1875–1882. 21
-
(2007)
Bioinformatics
, vol.23
, Issue.15
, pp. 1875-1882
-
-
Capra, J.A.1
Singh, M.2
-
18
-
-
58849142521
-
Finding and Characterizing Tunnels in Macromolecules with Application to Ion Channels and Pores
-
13
-
Coleman R.G., Sharp K.A.: Finding and Characterizing Tunnels in Macromolecules with Application to Ion Channels and Pores. Biophys. J. 96, 2 (2009), 632–645. 13
-
(2009)
Biophys. J.
, vol.96
, Issue.2
, pp. 632-645
-
-
Coleman, R.G.1
Sharp, K.A.2
-
19
-
-
29144467680
-
A Path Planning Approach for Computing Large-Amplitude Motions of Flexible Molecules
-
10, 19
-
Cortés J., Siméon T., Angulo V.R. d, Guieysse d., Remaud-Siméon M., Tran V.: A Path Planning Approach for Computing Large-Amplitude Motions of Flexible Molecules. Bioinformatics 21, suppl 1 (2005), i116–i125. 10, 19
-
(2005)
Bioinformatics
, vol.21
, pp. i116-i125
-
-
Cortés, J.1
Siméon, T.2
Angulo, V.R.D.3
Guieysse, D.4
Remaud-Siméon, M.5
Tran, V.6
-
20
-
-
84942753012
-
PrinCCes: Continuity-based geometric decomposition and systematic visualization of the void repertoire of proteins
-
12, 15, 21
-
Czirják G.: PrinCCes: Continuity-based geometric decomposition and systematic visualization of the void repertoire of proteins. J. Mol. Graph. Modell. 62 (2015), 118–127. 12, 15, 21
-
(2015)
J. Mol. Graph. Modell.
, vol.62
, pp. 118-127
-
-
Czirják, G.1
-
21
-
-
84883591293
-
MoMA-LigPath: a web server to simulate protein-ligand unbinding
-
19, 21
-
Devaurs D., Bouard L., Vaisset M., Zanon C., Al-Bluwi I., Iehl R., Siméon T., Cortés J.: MoMA-LigPath: a web server to simulate protein-ligand unbinding. Nucl. Acids Res. 41 (2013), 297–302. 19, 21
-
(2013)
Nucl. Acids Res.
, vol.41
, pp. 297-302
-
-
Devaurs, D.1
Bouard, L.2
Vaisset, M.3
Zanon, C.4
Al-Bluwi, I.5
Iehl, R.6
Siméon, T.7
Cortés, J.8
-
22
-
-
61449136202
-
Molecular docking algorithms
-
4
-
Dias R., de Azevedo J., Walter F.: Molecular docking algorithms. Current Drug Targets 9, 12 (2008), 1040–1047. 4
-
(2008)
Current Drug Targets
, vol.9
, Issue.12
, pp. 1040-1047
-
-
Dias, R.1
de Azevedo, J.2
Walter, F.3
-
23
-
-
79751535059
-
POVME: an algorithm for measuring binding-pocket volumes
-
8
-
Durrant J.D., de Oliveira C.A., McCammon J.A.: POVME: an algorithm for measuring binding-pocket volumes. J. Mol. Graph. Model. 29, 5 (2011), 773–776. 8
-
(2011)
J. Mol. Graph. Model.
, vol.29
, Issue.5
, pp. 773-776
-
-
Durrant, J.D.1
de Oliveira, C.A.2
McCammon, J.A.3
-
24
-
-
0346945148
-
PyMOL: An Open-Source Molecular Graphics Tool
-
15
-
DeLano W.L.: PyMOL: An Open-Source Molecular Graphics Tool. CCP4 Newsletter On Protein Crystallography 40 (2002). http://pymol.sourceforge.net/. 15
-
(2002)
CCP4 Newsletter On Protein Crystallography
, vol.40
-
-
DeLano, W.L.1
-
25
-
-
84949114871
-
Principal Component Analysis reveals correlation of cavities evolution and functional motions in proteins
-
(Feb, 8, 14
-
Desdouits N., Nilges M., Blondel A.: Principal Component Analysis reveals correlation of cavities evolution and functional motions in proteins. J. Mol. Graph. Model. 55 (Feb 2015), 13–24. 8, 14
-
(2015)
J. Mol. Graph. Model.
, vol.55
, pp. 13-24
-
-
Desdouits, N.1
Nilges, M.2
Blondel, A.3
-
26
-
-
33747818007
-
CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
-
21
-
Dundas J., Ouyang Z., Tseng J., Binkowski T.A., Turpaz Y., Liang J.: CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res. 34, Issue suppl 2 (2006), 116–118. 21
-
(2006)
Nucleic Acids Res.
, vol.34
, Issue.Issue
, pp. 116-118
-
-
Dundas, J.1
Ouyang, Z.2
Tseng, J.3
Binkowski, T.A.4
Turpaz, Y.5
Liang, J.6
-
27
-
-
84909619181
-
POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics
-
8
-
Durrant J.D., Votapka L., Sorensen J., Amaro R.E.: POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics. J Chem Theory Comput 10, 11 (2014), 5047–5056. 8
-
(2014)
J Chem Theory Comput
, vol.10
, Issue.11
, pp. 5047-5056
-
-
Durrant, J.D.1
Votapka, L.2
Sorensen, J.3
Amaro, R.E.4
-
28
-
-
0033482642
-
Deformable Smooth Surface Design
-
11
-
Edelsbrunner H.: Deformable Smooth Surface Design. Discrete Comput. Geom. 21, 1 (1999), 87–115. 11
-
(1999)
Discrete Comput. Geom.
, vol.21
, Issue.1
, pp. 87-115
-
-
Edelsbrunner, H.1
-
29
-
-
85053919378
-
Measuring Proteins and Voids in Proteins
-
In, 11
-
Edelsbrunner H., Facello M., Fu P., Liang J.: Measuring Proteins and Voids in Proteins. In Proceedings of the 28th Annual Hawaii International Conference on System Sciences (1995), vol. 5, pp. 256–264. 11
-
(1995)
Proceedings of the 28th Annual Hawaii International Conference on System Sciences
, vol.5
, pp. 256-264
-
-
Edelsbrunner, H.1
Facello, M.2
Fu, P.3
Liang, J.4
-
31
-
-
84949233236
-
Ligand binding mechanism in steroid receptors: From conserved plasticity to differential evolutionary constraints
-
4
-
Edman K., Hosseini A., Bjursell M.K., Aagaard A., Wissler L., Gunnarsson A., Kaminski T., Köhler C., Bäckström S., Jensen T.J., et al.: Ligand binding mechanism in steroid receptors: From conserved plasticity to differential evolutionary constraints. Structure 23, 12 (2015), 2280–2290. 4
-
(2015)
Structure
, vol.23
, Issue.12
, pp. 2280-2290
-
-
Edman, K.1
Hosseini, A.2
Bjursell, M.K.3
Aagaard, A.4
Wissler, L.5
Gunnarsson, A.6
Kaminski, T.7
Köhler, C.8
Bäckström, S.9
Jensen, T.J.10
-
32
-
-
0038592455
-
Identification of Substrate Channels and Protein Cavities
-
13
-
Exner T., Keil M., Möckel G., Brickmann J.: Identification of Substrate Channels and Protein Cavities. J. Mol. Model. 4, 10 (1998), 340–343. 13
-
(1998)
J. Mol. Model.
, vol.4
, Issue.10
, pp. 340-343
-
-
Exner, T.1
Keil, M.2
Möckel, G.3
Brickmann, J.4
-
33
-
-
84986483798
-
The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies
-
14
-
Eisenhaber F., Lijnzaad P., Argos P., Sander C., Scharf M.: The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies. J. Comput. Chem. 16, 3 (1995), 273–284. 14
-
(1995)
J. Comput. Chem.
, vol.16
, Issue.3
, pp. 273-284
-
-
Eisenhaber, F.1
Lijnzaad, P.2
Argos, P.3
Sander, C.4
Scharf, M.5
-
35
-
-
84979036583
-
MIMTool: A Tool for Drawing Molecular Interaction Maps
-
In,). arXiv 1407.2073. 4
-
Edes M., Özturan C., Haliloğlu T., Luna A., Nussinov R.: MIMTool: A Tool for Drawing Molecular Interaction Maps. In IEEE Symposium on Biological Data Visualization (2014). arXiv: 1407.2073. 4
-
(2014)
IEEE Symposium on Biological Data Visualization
-
-
Edes, M.1
Özturan, C.2
Haliloğlu, T.3
Luna, A.4
Nussinov, R.5
-
36
-
-
84892166712
-
Einfluss der Configuration auf die Wirkung der Enzyme
-
4
-
Fischer E.: Einfluss der Configuration auf die Wirkung der Enzyme. Ber. Dtsch. Chem. Ges. 27, 3 (1894), 2985–2993. 4
-
(1894)
Ber. Dtsch. Chem. Ges.
, vol.27
, Issue.3
, pp. 2985-2993
-
-
Fischer, E.1
-
37
-
-
84920804485
-
MegaMol – A Prototyping Framework for Particle-based Visualization
-
15, 16
-
Grottel S., Krone M., Müller C., Reina G., Ertl T.: MegaMol – A Prototyping Framework for Particle-based Visualization. IEEE Trans. Vis. Comput. Graphics 21, 2 (2015), 201–214. 15, 16
-
(2015)
IEEE Trans. Vis. Comput. Graphics
, vol.21
, Issue.2
, pp. 201-214
-
-
Grottel, S.1
Krone, M.2
Müller, C.3
Reina, G.4
Ertl, T.5
-
38
-
-
84860686811
-
Object-Space Ambient Occlusion for Molecular Dynamics
-
In, 13, 18
-
Grottel S., Krone M., Scharnowski K., Ertl T.: Object-Space Ambient Occlusion for Molecular Dynamics. In IEEE Pacific Visualization Symposium (2012), pp. 209–216. 13, 18
-
(2012)
IEEE Pacific Visualization Symposium
, pp. 209-216
-
-
Grottel, S.1
Krone, M.2
Scharnowski, K.3
Ertl, T.4
-
39
-
-
78449289709
-
Fast Surface-Based Travel Depth Estimation Algorithm for Macromolecule Surface Shape Description
-
18
-
Giard J., Rondao Alface P., Gala J.-L., Macq B.: Fast Surface-Based Travel Depth Estimation Algorithm for Macromolecule Surface Shape Description. IEEE/ACM Trans. Comput. Biol. Bioinformatics 8, 1 (2011), 59–68. 18
-
(2011)
IEEE/ACM Trans. Comput. Biol. Bioinformatics
, vol.8
, Issue.1
, pp. 59-68
-
-
Giard, J.1
Rondao Alface, P.2
Gala, J.-L.3
Macq, B.4
-
40
-
-
0033168847
-
MolSurfer: two-dimensional maps for navigating three-dimensional structures of proteins
-
(Jul, 4
-
Gabdoulline R.R., Wade R.C., Walther D.: MolSurfer: two-dimensional maps for navigating three-dimensional structures of proteins. Trends Biochem. Sci. 24, 7 (Jul 1999), 285–287. 4
-
(1999)
Trends Biochem. Sci.
, vol.24
, Issue.7
, pp. 285-287
-
-
Gabdoulline, R.R.1
Wade, R.C.2
Walther, D.3
-
41
-
-
33947420470
-
New method for fast and accurate binding-site identification and analysis
-
20
-
Halgren T.: New method for fast and accurate binding-site identification and analysis. Chem Biol Drug Des 69, 2 (2007), 146–148. 20
-
(2007)
Chem Biol Drug Des
, vol.69
, Issue.2
, pp. 146-148
-
-
Halgren, T.1
-
42
-
-
65249117514
-
Identifying and characterizing binding sites and assessing druggability
-
20
-
Halgren T.A.: Identifying and characterizing binding sites and assessing druggability. J Chem Inf Model 49, 2 (2009), 377–389. 20
-
(2009)
J Chem Inf Model
, vol.49
, Issue.2
, pp. 377-389
-
-
Halgren, T.A.1
-
44
-
-
0029878720
-
VMD – Visual Molecular Dynamics
-
15, 16
-
Humphrey W., Dalke A., Schulten K.: VMD – Visual Molecular Dynamics. J. Mol. Graph. 14 (1996), 33–38. 15, 16
-
(1996)
J. Mol. Graph.
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
45
-
-
57649229060
-
HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures
-
12, 21
-
Ho B.K., Gruswitz F.: HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures. BMC Struct. Biol. 8, 1 (2008), 49+. 12, 21
-
(2008)
BMC Struct. Biol.
, vol.8
, Issue.1
, pp. 49+
-
-
Ho, B.K.1
Gruswitz, F.2
-
46
-
-
67849097355
-
SITEHOUNDweb: a server for ligand binding site identification in protein structures
-
6, 21
-
Hernandez M., Ghersi D., Sanchez R.: SITEHOUNDweb: a server for ligand binding site identification in protein structures. Nucleic Acids Res. 37, suppl 2 (2009), W413–W416. 6, 21
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. W413-W416
-
-
Hernandez, M.1
Ghersi, D.2
Sanchez, R.3
-
47
-
-
84908087033
-
Visualising Intrinsic Disorder and Conformational Variation in Protein Ensembles
-
4
-
Heinrich J., Krone M., O'Donoghue S.I., Weiskopf D.: Visualising Intrinsic Disorder and Conformational Variation in Protein Ensembles. Faraday Discuss. 169 (2014), 179–193. 4
-
(2014)
Faraday Discuss.
, vol.169
, pp. 179-193
-
-
Heinrich, J.1
Krone, M.2
O'Donoghue, S.I.3
Weiskopf, D.4
-
48
-
-
0031370977
-
LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins
-
12, 13, 21
-
Hendlich M., Rippmann F., Barnickel G.: LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J. Mol. Graphics Modell. 15, 6 (1997), 359–363. 12, 13, 21
-
(1997)
J. Mol. Graphics Modell.
, vol.15
, Issue.6
, pp. 359-363
-
-
Hendlich, M.1
Rippmann, F.2
Barnickel, G.3
-
49
-
-
33750029942
-
LIGSITEcsc: Predicting Ligand Binding Sites Using the Connolly Surface and Degree of Conservation
-
12, 21
-
Huang B., Schroeder M.: LIGSITEcsc: Predicting Ligand Binding Sites Using the Connolly Surface and Degree of Conservation. BMC Structural Biology 6, 1 (2006), 19. 12, 21
-
(2006)
BMC Structural Biology
, vol.6
, Issue.1
, pp. 19
-
-
Huang, B.1
Schroeder, M.2
-
50
-
-
76049105287
-
Navigating molecular worms inside chemical labyrinths
-
7
-
Haranczyk M., Sethian J.A.: Navigating molecular worms inside chemical labyrinths. Proc. Natl. Acad. Sci. USA 106, 51 (2009), 21472–21477. 7
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, Issue.51
, pp. 21472-21477
-
-
Haranczyk, M.1
Sethian, J.A.2
-
51
-
-
69249150494
-
MetaPocket: a meta approach to improve protein ligand binding site prediction
-
21
-
Huang B.: MetaPocket: a meta approach to improve protein ligand binding site prediction. Omics 13(4) (2009), 325–330. 21
-
(2009)
Omics 13(4)
, pp. 325-330
-
-
Huang, B.1
-
52
-
-
84906324850
-
Search strategies and evaluation in protein-protein docking: principles, advances and challenges
-
4
-
Huang S.-Y.: Search strategies and evaluation in protein-protein docking: principles, advances and challenges. Drug Discov. Today 19, 8 (2014), 1081–1096. 4
-
(2014)
Drug Discov. Today
, vol.19
, Issue.8
, pp. 1081-1096
-
-
Huang, S.-Y.1
-
53
-
-
84908102015
-
A real-time proximity querying algorithm for haptic-based molecular docking
-
4
-
Iakovou G., Hayward S., Laycock S.: A real-time proximity querying algorithm for haptic-based molecular docking. Faraday Discuss. 169 (2014), 359–377. 4
-
(2014)
Faraday Discuss.
, vol.169
, pp. 359-377
-
-
Iakovou, G.1
Hayward, S.2
Laycock, S.3
-
54
-
-
0036022961
-
Q-fit: A probabilistic method for docking molecular fragments by sampling low energy conformational space
-
6
-
Jackson R.M.: Q-fit: A probabilistic method for docking molecular fragments by sampling low energy conformational space. J. Comput. Aided Mol. Des. 16, 1 (2002), 43–57. 6
-
(2002)
J. Comput. Aided Mol. Des.
, vol.16
, Issue.1
, pp. 43-57
-
-
Jackson, R.M.1
-
56
-
-
84973644945
-
Accelerated Visualization of Transparent Molecular Surfaces in Molecular Dynamics
-
In,). 13, 16
-
Jurčík A., Parulek J., Sochor J., Kozlíková B.: Accelerated Visualization of Transparent Molecular Surfaces in Molecular Dynamics. In IEEE Pacific Visualization Symposium (2016). 13, 16
-
(2016)
IEEE Pacific Visualization Symposium
-
-
Jurčík, A.1
Parulek, J.2
Sochor, J.3
Kozlíková, B.4
-
57
-
-
84891850975
-
Targeting Protein-Protein Interaction by Small Molecules
-
4
-
Jin L., Wang W., Fang G.: Targeting Protein-Protein Interaction by Small Molecules. Annu. Rev. Pharmacool. Toxicol. 54, 1 (2014), 435–456. 4
-
(2014)
Annu. Rev. Pharmacool. Toxicol.
, vol.54
, Issue.1
, pp. 435-456
-
-
Jin, L.1
Wang, W.2
Fang, G.3
-
58
-
-
77951217659
-
Detection of multiscale pockets on protein surfaces using mathematical morphology
-
12, 21
-
Kawabata T.: Detection of multiscale pockets on protein surfaces using mathematical morphology. Proteins: Struct., Funct., Bioinf. 78, 5 (2010), 1195–1211. 12, 21
-
(2010)
Proteins: Struct., Funct., Bioinf.
, vol.78
, Issue.5
, pp. 1195-1211
-
-
Kawabata, T.1
-
59
-
-
30044440098
-
Molecular Interaction Maps of Bioregulatory Networks: A General Rubric for Systems Biology
-
4
-
Kohn K.w., Aladjem M.I., Weinstein J.N., Pommier Y.: Molecular Interaction Maps of Bioregulatory Networks: A General Rubric for Systems Biology. Mol. Biol. Cell. 17, 1 (2006), 1–13. 4
-
(2006)
Mol. Biol. Cell.
, vol.17
, Issue.1
, pp. 1-13
-
-
Kohn, K.W.1
Aladjem, M.I.2
Weinstein, J.N.3
Pommier, Y.4
-
60
-
-
84892778855
-
Tunnels and Voids in Molecules via Voronoi Diagrams and Beta-Complexes Transactions on Computational Science XX
-
In, Gavrilova M.L., Tan C. J. K., Kalantari B., (Eds.),, Springer, Berlin Heidelberg, 11
-
Kim D.-S., Cho Y., Kim J.-K., Sugihara K.: Tunnels and Voids in Molecules via Voronoi Diagrams and Beta-Complexes. In Transactions on Computational Science XX, Gavrilova M.L., Tan C. J. K., Kalantari B., (Eds.), no. 8110 in Lecture Notes in Computer Science. Springer Berlin Heidelberg, 2013, pp. 92–111. 11
-
(2013)
no. 8110 in Lecture Notes in Computer Science
, pp. 92-111
-
-
Kim, D.-S.1
Cho, Y.2
Kim, J.-K.3
Sugihara, K.4
-
61
-
-
84979850720
-
BetaCavityWeb: a webserver for molecular voids and channels
-
gkv360. 21
-
Kim J.-K., Cho Y., Lee M., Laskowski R.A., Ryu S.E., Sugihara K., Kim D.-S.: BetaCavityWeb: a webserver for molecular voids and channels. Nucl. Acids Res. (2015), gkv360. 21
-
(2015)
Nucl. Acids Res.
-
-
Kim, J.-K.1
Cho, Y.2
Lee, M.3
Laskowski, R.A.4
Ryu, S.E.5
Sugihara, K.6
Kim, D.-S.7
-
62
-
-
84860694891
-
Interactive Exploration of Protein Cavities
-
7, 15
-
Krone M., Falk M., Rehm S., Pleiss J., Ertl T.: Interactive Exploration of Protein Cavities. Comput. Graph. Forum 30, 3 (2011), 673–682. 7, 15
-
(2011)
Comput. Graph. Forum
, vol.30
, Issue.3
, pp. 673-682
-
-
Krone, M.1
Falk, M.2
Rehm, S.3
Pleiss, J.4
Ertl, T.5
-
64
-
-
84856370676
-
Pocketome: an encyclopedia of small-molecule binding sites in 4d
-
Database issue (, 20
-
Kufareva I., Ilatovskiy A.V., Abagyan R.: Pocketome: an encyclopedia of small-molecule binding sites in 4d. Nucleic Acids Res. 40, Database issue (2012), D535–540. 20
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D535-540
-
-
Kufareva, I.1
Ilatovskiy, A.V.2
Abagyan, R.3
-
65
-
-
0027995683
-
Detection, delineation, measurement and display of cavities in macromolecular structures
-
13, 21
-
Kleywegt G.J., Jones T.A.: Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Crystallogr., Sect D: Biol. Crystallogr. 50, 2 (1994), 178–185. 13, 21
-
(1994)
Acta Crystallogr., Sect D: Biol. Crystallogr.
, vol.50
, Issue.2
, pp. 178-185
-
-
Kleywegt, G.J.1
Jones, T.A.2
-
66
-
-
85039057990
-
Visualization of Biomolecular Structures: State of the Art
-
In, 1, 12, 18
-
Kozlíková B., Krone M., Lindow N., Falk M., Baaden M., Baum D., Viola I., Parulek J., Hege H.-C.: Visualization of Biomolecular Structures: State of the Art. In Eurographics Conference on Visualization – STARs (2015), pp. 61–81. 1, 12, 18
-
(2015)
Eurographics Conference on Visualization – STARs
, pp. 61-81
-
-
Kozlíková, B.1
Krone, M.2
Lindow, N.3
Falk, M.4
Baaden, M.5
Baum, D.6
Viola, I.7
Parulek, J.8
Hege, H.-C.9
-
67
-
-
84899523764
-
Visual Analysis of Dynamic Protein Cavities and Binding Sites
-
In, 13, 15, 16, 17, 21
-
Krone M., Kauker D., Reina G., Ertl T.: Visual Analysis of Dynamic Protein Cavities and Binding Sites. In IEEE PacificVis-Visualization Notes (2014), vol. 1, pp. 301–305. 13, 15, 16, 17, 21
-
(2014)
IEEE PacificVis-Visualization Notes
, vol.1
, pp. 301-305
-
-
Krone, M.1
Kauker, D.2
Reina, G.3
Ertl, T.4
-
68
-
-
84903545297
-
Ensemble generation and the influence of protein flexibility on geometric tunnel prediction in cytochrome P450 enzymes
-
9
-
Kingsley L.J., Lill M.A.: Ensemble generation and the influence of protein flexibility on geometric tunnel prediction in cytochrome P450 enzymes. PLoS ONE 9, 6 (2014), e99408. 9
-
(2014)
PLoS ONE
, vol.9
, Issue.6
-
-
Kingsley, L.J.1
Lill, M.A.2
-
69
-
-
84953835133
-
GPU Accelerated Finding of Channels and Tunnels for a Protein Molecule
-
(First online 2014). 9, 15
-
KIM B., Lee J.E., Kim Y.J., Kim K.-J.: GPU Accelerated Finding of Channels and Tunnels for a Protein Molecule. Int. J. Parallel. Prog. 44, 1 (2016), 87–108. (First online: 2014). 9, 15
-
(2016)
Int. J. Parallel. Prog.
, vol.44
, Issue.1
, pp. 87-108
-
-
Kim, B.1
Lee, J.E.2
Kim, Y.J.3
Kim, K.-J.4
-
70
-
-
84878181372
-
TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins
-
8, 19, 21
-
Kokh D.B., Richter S., Henrich S., Czodrowski P., Rippmann F., Wade R.C.: TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins. J. Chem. Inf. Model. 53, 5 (2013), 1235–1252. 8, 19, 21
-
(2013)
J. Chem. Inf. Model.
, vol.53
, Issue.5
, pp. 1235-1252
-
-
Kokh, D.B.1
Richter, S.2
Henrich, S.3
Czodrowski, P.4
Rippmann, F.5
Wade, R.C.6
-
71
-
-
84879764717
-
Interactive Extraction and Tracking of Biomolecular Surface Features
-
13, 17
-
Krone M., Reina G., Schulz C., Kulschewski T., Pleiss J., Ertl T.: Interactive Extraction and Tracking of Biomolecular Surface Features. Comput. Graph. Forum 32, 3 (2013), 331–340. 13, 17
-
(2013)
Comput. Graph. Forum
, vol.32
, Issue.3
, pp. 331-340
-
-
Krone, M.1
Reina, G.2
Schulz, C.3
Kulschewski, T.4
Pleiss, J.5
Ertl, T.6
-
72
-
-
84875929674
-
Fast Visualization of Gaussian Density Surfaces for Molecular Dynamics and Particle System Trajectories
-
In, 13
-
Krone M., Stone J.E., Ertl T., Schulten K.: Fast Visualization of Gaussian Density Surfaces for Molecular Dynamics and Particle System Trajectories. In EuroVis-Short Papers (2012), vol. 1, pp. 67–71. 13
-
(2012)
EuroVis-Short Papers
, vol.1
, pp. 67-71
-
-
Krone, M.1
Stone, J.E.2
Ertl, T.3
Schulten, K.4
-
73
-
-
84908088475
-
YASARA View—molecular graphics for all devices—from smartphones to workstations
-
20
-
Krieger E., Vriend G.: YASARA View—molecular graphics for all devices—from smartphones to workstations. Bioinformatics 30, 20 (2014), 2981–2982. 20
-
(2014)
Bioinformatics
, vol.30
, Issue.20
, pp. 2981-2982
-
-
Krieger, E.1
Vriend, G.2
-
74
-
-
84907481670
-
CAVER Analyst 1.0: Graphic tool for interactive visualization and analysis of tunnels and channels in protein structures
-
9, 15, 16, 21
-
Kozlíková B., Šebestová E., Šustr V., Brezovský J., Strnad O., Daniel L., Bednář D., Pavelka A., Maňák M., Bezděka M., Beneš P., Kotry M., Gora A., Damborský J., Sochor J.: CAVER Analyst 1.0: Graphic tool for interactive visualization and analysis of tunnels and channels in protein structures. Bioinformatics 30, 18 (2014), btu364. 9, 15, 16, 21
-
(2014)
Bioinformatics
, vol.30
, Issue.18
, pp. btu364
-
-
Kozlíková, B.1
Šebestová, E.2
Šustr, V.3
Brezovský, J.4
Strnad, O.5
Daniel, L.6
Bednář, D.7
Pavelka, A.8
Maňák, M.9
Bezděka, M.10
Beneš, P.11
Kotry, M.12
Gora, A.13
Damborský, J.14
Sochor, J.15
-
75
-
-
45349108801
-
Functional classification of protein kinase binding sites using Cavbase
-
20
-
Kuhn D., Weskamp N., Hullermeier E., Klebe G.: Functional classification of protein kinase binding sites using Cavbase. ChemMedChem 2, 10 (2007), 1432–1447. 20
-
(2007)
ChemMedChem
, vol.2
, Issue.10
, pp. 1432-1447
-
-
Kuhn, D.1
Weskamp, N.2
Hullermeier, E.3
Klebe, G.4
-
76
-
-
0028881975
-
SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions
-
10, 12, 21
-
Laskowski R.A.: SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions. J. Mol. Graphics 13, 5 (1995), 323–330. 10, 12, 21
-
(1995)
J. Mol. Graphics
, vol.13
, Issue.5
, pp. 323-330
-
-
Laskowski, R.A.1
-
78
-
-
0027053611
-
POCKET: A Computer Graphics Method for Identifying and Displaying Protein Cavities and Their Surrounding Amino Acids
-
5, 6, 21
-
Levitt D.G., BanaszakL. J.: POCKET: A Computer Graphics Method for Identifying and Displaying Protein Cavities and Their Surrounding Amino Acids. J. Mol. Graph. 10, 4 (1992), 229–234. 5, 6, 21
-
(1992)
J. Mol. Graph.
, vol.10
, Issue.4
, pp. 229-234
-
-
Levitt, D.G.1
BanaszakL., J.2
-
79
-
-
84872252594
-
Dynamic Channels in Biomolecular Systems: Path Analysis and Visualization
-
In, 11, 16
-
Lindow N., Baum D., Bondar A.-N., Hege H.-C.: Dynamic Channels in Biomolecular Systems: Path Analysis and Visualization. In IEEE Symposium on Biological Data Visualization (2012), pp. 99–106. 11, 16
-
(2012)
IEEE Symposium on Biological Data Visualization
, pp. 99-106
-
-
Lindow, N.1
Baum, D.2
Bondar, A.-N.3
Hege, H.-C.4
-
80
-
-
84899908873
-
Exploring cavity dynamics in biomolecular systems
-
11, 16, 17
-
Lindow N., Baum D., Bondar A.-N., Hege H.-C.: Exploring cavity dynamics in biomolecular systems. BMC Bioinformatics 14, Suppl 19 (2013), S5. 11, 16, 17
-
(2013)
BMC Bioinformatics
, vol.14
, pp. S5
-
-
Lindow, N.1
Baum, D.2
Bondar, A.-N.3
Hege, H.-C.4
-
81
-
-
80855130019
-
Voronoi-Based Extraction and Visualization of Molecular Paths
-
11, 16
-
Lindow N., Baum D., Hege H.-C.: Voronoi-Based Extraction and Visualization of Molecular Paths. IEEE Trans. Vis. Comput. Graphics 17, 12 (2011), 2025–2034. 11, 16
-
(2011)
IEEE Trans. Vis. Comput. Graphics
, vol.17
, Issue.12
, pp. 2025-2034
-
-
Lindow, N.1
Baum, D.2
Hege, H.-C.3
-
82
-
-
84910049935
-
Ligand Excluded Surface: A New Type of Molecular Surface
-
14, 19
-
Lindow N., Baum D., Hege H.-C.: Ligand Excluded Surface: A New Type of Molecular Surface. IEEE Trans. Vis. Comput. Graphics 20, 12 (2014), 2486–2495. 14, 19
-
(2014)
IEEE Trans. Vis. Comput. Graphics
, vol.20
, Issue.12
, pp. 2486-2495
-
-
Lindow, N.1
Baum, D.2
Hege, H.-C.3
-
83
-
-
77955729034
-
Accelerated Visualization of Dynamic Molecular Surfaces
-
11
-
Lindow N., Baum D., Prohaska S., Hege H.-C.: Accelerated Visualization of Dynamic Molecular Surfaces. Comput. Graph. Forum 29, 3 (2010), 943–952. 11
-
(2010)
Comput. Graph. Forum
, vol.29
, Issue.3
, pp. 943-952
-
-
Lindow, N.1
Baum, D.2
Prohaska, S.3
Hege, H.-C.4
-
85
-
-
84946174179
-
Epock: rapid analysis of protein pocket dynamics
-
8, 21
-
Laurent B., Chavent M., Cragnolini T., Dahl A. C E, Pasquali S., Derreumaux P., Sansom M. S. P., Baaden M.: Epock: rapid analysis of protein pocket dynamics. Bioinformatics 31, 9 (2015), 1478–1480. 8, 21
-
(2015)
Bioinformatics
, vol.31
, Issue.9
, pp. 1478-1480
-
-
Laurent, B.1
Chavent, M.2
Cragnolini, T.3
Dahl, A.C.E.4
Pasquali, S.5
Derreumaux, P.6
Sansom, M.S.P.7
Baaden, M.8
-
86
-
-
0032190305
-
Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape
-
11
-
Liang J., Edelsbrunner H., Fu P., Sudhakar P.V., Subramaniam S.: Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape. Proteins 33, 1 (1998), 1–17. 11
-
(1998)
Proteins
, vol.33
, Issue.1
, pp. 1-17
-
-
Liang, J.1
Edelsbrunner, H.2
Fu, P.3
Sudhakar, P.V.4
Subramaniam, S.5
-
87
-
-
0032189626
-
Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins
-
11
-
Liang J., Edelsbrunner H., Fu P., Sudhakar P.V., Subramaniam S.: Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins. Proteins 33, 1 (1998), 18–29. 11
-
(1998)
Proteins
, vol.33
, Issue.1
, pp. 18-29
-
-
Liang, J.1
Edelsbrunner, H.2
Fu, P.3
Sudhakar, P.V.4
Subramaniam, S.5
-
88
-
-
0031687653
-
Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design
-
10, 11, 12, 21
-
Liang J., Edelsbrunner H., Woodward C.: Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein science: a publication of the Protein Society 7, 9 (1998), 1884–1897. 10, 11, 12, 21
-
(1998)
Protein science: a publication of the Protein Society
, vol.7
, Issue.9
, pp. 1884-1897
-
-
Liang, J.1
Edelsbrunner, H.2
Woodward, C.3
-
89
-
-
67649422714
-
Fpocket: An open source platform for ligand pocket detection
-
9, 11, 15,21
-
Le Guilloux V., Schmidtke P., Tuffery P.: Fpocket: An open source platform for ligand pocket detection. BMC Bioinformatics 10, 1 (2009), 168. 9, 11, 15,21
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.1
, pp. 168
-
-
Le Guilloux, V.1
Schmidtke, P.2
Tuffery, P.3
-
90
-
-
18744394070
-
Q-SiteFinder: an energybased method for the prediction of protein-ligand binding sites
-
(May, 6, 21
-
Laurie A. T. R., Jackson R.M.: Q-SiteFinder: an energybased method for the prediction of protein-ligand binding sites. Bioinformatics 21, 9 (May 2005), 1908–1916. 6, 21
-
(2005)
Bioinformatics
, vol.21
, Issue.9
, pp. 1908-1916
-
-
Laurie, A.T.R.1
Jackson, R.M.2
-
91
-
-
84979042576
-
Computing and Displaying Intermolecular Negative Volume for Docking Scientific Visualization: The Visual Extraction of Knowledge from Data
-
In, Bonneau G.-P., Ertl T., Nielson G.M., (Eds.),, Springer, 4
-
Lee C.H., Varshney A.: Computing and Displaying Intermolecular Negative Volume for Docking. In Scientific Visualization: The Visual Extraction of Knowledge from Data, Bonneau G.-P., Ertl T., Nielson G.M., (Eds.), Mathematics and Visualization. Springer, 2006, pp. 49–64. 4
-
(2006)
Mathematics and Visualization
, pp. 49-64
-
-
Lee, C.H.1
Varshney, A.2
-
92
-
-
84861407812
-
Computation of tunnels in protein molecules using Delaunay triangulation
-
8, 9
-
Medek P., Beneš P., Sochor J.: Computation of tunnels in protein molecules using Delaunay triangulation. Journal of WSCG 15(1-3) (2007), 107–114. 8, 9
-
(2007)
Journal of WSCG 15(1-3)
, pp. 107-114
-
-
Medek, P.1
Beneš, P.2
Sochor, J.3
-
93
-
-
84934275733
-
Multi-modal perceptualization of volumetric data and its application to molecular docking
-
In, 4
-
Maciejewski R., Choi S., Ebert D.S., Tan H.Z.: Multi-modal perceptualization of volumetric data and its application to molecular docking. In First Joint Eurohaptics Conference and Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems. World Haptics Conference (2005), pp. 511–514. 4
-
(2005)
First Joint Eurohaptics Conference and Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems. World Haptics Conference
, pp. 511-514
-
-
Maciejewski, R.1
Choi, S.2
Ebert, D.S.3
Tan, H.Z.4
-
94
-
-
58849118376
-
Development of new indices to evaluate protein-protein interfaces: Assembling space volume, assembling space distance, and global shape descriptor
-
4
-
Maeda M.H., Kinoshita K.: Development of new indices to evaluate protein-protein interfaces: Assembling space volume, assembling space distance, and global shape descriptor. J. Mol. Graph. Modell. 27, 6 (2009), 706–711. 4
-
(2009)
J. Mol. Graph. Modell.
, vol.27
, Issue.6
, pp. 706-711
-
-
Maeda, M.H.1
Kinoshita, K.2
-
95
-
-
84928561542
-
CHEXVIS: a tool for molecular channel extraction and visualization
-
11, 16, 17, 20, 21
-
Masood T.B., Sandhya S., Chandra N., Natarajan V.: CHEXVIS: a tool for molecular channel extraction and visualization. BMC Bioinformatics 16 (2015), 119. 11, 16, 17, 20, 21
-
(2015)
BMC Bioinformatics
, vol.16
, pp. 119
-
-
Masood, T.B.1
Sandhya, S.2
Chandra, N.3
Natarajan, V.4
-
96
-
-
79959224583
-
Molecular docking: A powerful approach for structure-based drug discovery
-
4
-
Meng X.-Y., Zhang H.-X., Mezei M., Cui M.: Molecular docking: A powerful approach for structure-based drug discovery. Current Computer Aided-Drug Design 7, 2 (2011), 146–157. 4
-
(2011)
Current Computer Aided-Drug Design
, vol.7
, Issue.2
, pp. 146-157
-
-
Meng, X.-Y.1
Zhang, H.-X.2
Mezei, M.3
Cui, M.4
-
97
-
-
33745595594
-
Segmenting Molecular Surfaces
-
18
-
Natarajan V., Wang Y., Bremer P.T., Pascucci V., Hamann B.: Segmenting Molecular Surfaces. Comput. Aided, Geom. D. 23, 6 (2006), 495–509. 18
-
(2006)
Comput. Aided, Geom. D.
, vol.23
, Issue.6
, pp. 495-509
-
-
Natarajan, V.1
Wang, Y.2
Bremer, P.T.3
Pascucci, V.4
Hamann, B.5
-
98
-
-
84902300574
-
Kvfinder: steered identification of protein cavities as a pymol plugin
-
14
-
Oliveira S.H., Ferraz F.A., Honorato R.V., Xavier-Neto J., Sobreira T.J., de Oliveira P.S.: Kvfinder: steered identification of protein cavities as a pymol plugin. BMC Bioinformatics 15, 1 (2014), 1–8. 14
-
(2014)
BMC Bioinformatics
, vol.15
, Issue.1
, pp. 1-8
-
-
Oliveira, S.H.1
Ferraz, F.A.2
Honorato, R.V.3
Xavier-Neto, J.4
Sobreira, T.J.5
de Oliveira, P.S.6
-
99
-
-
79951987069
-
Voroprot: an interactive tool for the analysis and visualization of complex geometric features of protein structure
-
11, 21
-
OlechnoviC K., Margelevicius M., Venclovas C.: Voroprot: an interactive tool for the analysis and visualization of complex geometric features of protein structure. Bioinformatics 27, 5 (2011), 723–724. 11, 21
-
(2011)
Bioinformatics
, vol.27
, Issue.5
, pp. 723-724
-
-
OlechnoviC, K.1
Margelevicius, M.2
Venclovas, C.3
-
100
-
-
67849130559
-
HotSpot Wizard: A Web Server for Identification of Hot Spots in Protein Engineering
-
21
-
Pavelka A., Chovancová E., Damborský J.: HotSpot Wizard: A Web Server for Identification of Hot Spots in Protein Engineering. Nucl. Acids Res. 37, 2 (2009), W376–383. 21
-
(2009)
Nucl. Acids Res.
, vol.37
, Issue.2
, pp. W376-383
-
-
Pavelka, A.1
Chovancová, E.2
Damborský, J.3
-
101
-
-
68249097450
-
PoreWalker: A Novel Tool for the Identification and Characterization of Channels in Transmembrane Proteins from Their Three-Dimensional Structure
-
16, 21
-
Pellegrini-Calace M., Maiwald T., Thornton J.M.: PoreWalker: A Novel Tool for the Identification and Characterization of Channels in Transmembrane Proteins from Their Three-Dimensional Structure. PLoS Comput. Biol. 5, 7 (2009), e1000440. 16, 21
-
(2009)
PLoS Comput. Biol.
, vol.5
, Issue.7
-
-
Pellegrini-Calace, M.1
Maiwald, T.2
Thornton, J.M.3
-
102
-
-
84900549764
-
Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories: trj_cavity
-
8
-
Paramo T., East A., Garzon B., Ulmschneider M.B., Bond P.J.: Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories: trj_cavity. J. Chem. Theory Comput. 10, 5 (2014), 2151–2164. 8
-
(2014)
J. Chem. Theory Comput.
, vol.10
, Issue.5
, pp. 2151-2164
-
-
Paramo, T.1
East, A.2
Garzon, B.3
Ulmschneider, M.B.4
Bond, P.J.5
-
103
-
-
84873546773
-
Engineering of Protein Tunnels: Keyhole-lock-key Model for Catalysis by the Enzymes with Buried Active Sites
-
In, Lutz S., Bornscheuer U., (Eds.)., Wiley-VCH, 4
-
Prokop Z., Gora A., Brezovsky J., Chaloupková R., StEpánková V., Damborsky J.: Engineering of Protein Tunnels: Keyhole-lock-key Model for Catalysis by the Enzymes with Buried Active Sites. In Protein Engineering Handbook, Lutz S., Bornscheuer U., (Eds.). Wiley-VCH, 2012, pp. 421–464. 4
-
(2012)
Protein Engineering Handbook
, pp. 421-464
-
-
Prokop, Z.1
Gora, A.2
Brezovsky, J.3
Chaloupková, R.4
StEpánková, V.5
Damborsky, J.6
-
104
-
-
77954077784
-
Measuring Properties of Molecular Surfaces Using Ray Casting
-
In,). 7, 15
-
Phillips M., Georgiev I., Dehof A.K., Nickels S., Marsalek L., Lenhof H.-P., Hildebrandt A., Slusallek P.: Measuring Properties of Molecular Surfaces Using Ray Casting. In Proc. Intl. Workshop on High Performance Computational Biology (2010). 7, 15
-
(2010)
Proc. Intl. Workshop on High Performance Computational Biology
-
-
Phillips, M.1
Georgiev, I.2
Dehof, A.K.3
Nickels, S.4
Marsalek, L.5
Lenhof, H.-P.6
Hildebrandt, A.7
Slusallek, P.8
-
105
-
-
4444221565
-
UCSF Chimera – A Visualization System for Exploratory Research and Analysis
-
15
-
Pettersen E.F., Goddard T.B., Huang C.C., Couch G.S., Greenblatt B.M., Meng E.C., Ferrin T.E.: UCSF Chimera – A Visualization System for Exploratory Research and Analysis. J. Comput. Chem. 25, 13 (2004), 1605–1612. 15
-
(2004)
J. Comput. Chem.
, vol.25
, Issue.13
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.B.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, B.M.5
Meng, E.C.6
Ferrin, T.E.7
-
106
-
-
35748972048
-
MOLE: A Voronoi Diagram-Based Explorer of Molecular Channels, Pores, and Tunnels
-
8, 9
-
Petřek M., Košinová P., Koča J., Otyepka M.: MOLE: A Voronoi Diagram-Based Explorer of Molecular Channels, Pores, and Tunnels. Structure 15, 11 (2007), 1357–1363. 8, 9
-
(2007)
Structure
, vol.15
, Issue.11
, pp. 1357-1363
-
-
Petřek, M.1
Košinová, P.2
Koča, J.3
Otyepka, M.4
-
107
-
-
33847142225
-
CAVER: A New Tool to Explore Routes From Protein Clefts, Pockets and Cavities
-
6, 8, 9, 21
-
Petřek M., Otyepka M., Banáš P., Košinová P., Koča J., Damborský J.: CAVER: A New Tool to Explore Routes From Protein Clefts, Pockets and Cavities. BMC Bioinform. 7, 1 (2006), 316. 6, 8, 9, 21
-
(2006)
BMC Bioinform.
, vol.7
, Issue.1
, pp. 316
-
-
Petřek, M.1
Otyepka, M.2
Banáš, P.3
Košinová, P.4
Koča, J.5
Damborský, J.6
-
108
-
-
84872239641
-
Implicit surfaces for interactive graph based cavity analysis of molecular simulations
-
In,). 13, 16
-
Parulek J., Turkay C., Reuter N., Viola I.: Implicit surfaces for interactive graph based cavity analysis of molecular simulations. In IEEE Symposium on Biological Data Visualization (2012). 13, 16
-
(2012)
IEEE Symposium on Biological Data Visualization
-
-
Parulek, J.1
Turkay, C.2
Reuter, N.3
Viola, I.4
-
109
-
-
84899970686
-
Visual cavity analysis in molecular simulations
-
13, 16
-
Parulek J., Turkay C., Reuter N., Viola I.: Visual cavity analysis in molecular simulations. BMC Bioinformatics 14, 19 (2013), 1–15. 13, 16
-
(2013)
BMC Bioinformatics
, vol.14
, Issue.19
, pp. 1-15
-
-
Parulek, J.1
Turkay, C.2
Reuter, N.3
Viola, I.4
-
110
-
-
84978978907
-
CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules
-
. 9
-
Pavelka A., Šebestová E., Kozlíková B., Brezovský J., Sochor J., Damborský J.: CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules. IEEE, ACM T. Comput. Bi. (2015). 9
-
(2015)
IEEE, ACM T. Comput. Bi.
-
-
Pavelka, A.1
Šebestová, E.2
Kozlíková, B.3
Brezovský, J.4
Sochor, J.5
Damborský, J.6
-
111
-
-
12844273672
-
Intersurf: dynamic interface between proteins
-
(Jan, 4
-
Ray N., Cavin X., Paul J.C., Maigret B.: Intersurf: dynamic interface between proteins. J. Mol. Graph. Model. 23, 4 (Jan 2005), 347–354. 4
-
(2005)
J. Mol. Graph. Model.
, vol.23
, Issue.4
, pp. 347-354
-
-
Ray, N.1
Cavin, X.2
Paul, J.C.3
Maigret, B.4
-
112
-
-
79955795138
-
dxTuber: Detecting Protein Cavities, Tunnels and Clefts Based on Protein and Solvent Dynamics
-
7, 9, 21
-
Raunest M., Kandt C.: dxTuber: Detecting Protein Cavities, Tunnels and Clefts Based on Protein and Solvent Dynamics. J. Mol. Graph. Modell. 29, 7 (2011), 895–905. 7, 9, 21
-
(2011)
J. Mol. Graph. Modell.
, vol.29
, Issue.7
, pp. 895-905
-
-
Raunest, M.1
Kandt, C.2
-
113
-
-
82255164267
-
MDpocket: Open-Source Cavity Detection and Characterization on Molecular Dynamics Trajectories
-
9, 21
-
Schmidtke P., Bidon-Chanal A., Luque F.J., Barril X.: MDpocket: Open-Source Cavity Detection and Characterization on Molecular Dynamics Trajectories. Bioinformatics 27, 23 (2011), 3276–3285. 9, 21
-
(2011)
Bioinformatics
, vol.27
, Issue.23
, pp. 3276-3285
-
-
Schmidtke, P.1
Bidon-Chanal, A.2
Luque, F.J.3
Barril, X.4
-
114
-
-
84945541907
-
A pipeline to enhance ligand virtual screening: Integrating molecular dynamics and fingerprints for ligand and proteins
-
PMID 26355717. 4
-
Spyrakis F., Benedetti P., Decherchi S., Rocchia W., Cavalli A., Alcaro S., Ortuso F., Baroni M., Cruciani G.: A pipeline to enhance ligand virtual screening: Integrating molecular dynamics and fingerprints for ligand and proteins. J Chem Inf Model 55, 10 (2015), 2256–2274. PMID: 26355717. 4
-
(2015)
J Chem Inf Model
, vol.55
, Issue.10
, pp. 2256-2274
-
-
Spyrakis, F.1
Benedetti, P.2
Decherchi, S.3
Rocchia, W.4
Cavalli, A.5
Alcaro, S.6
Ortuso, F.7
Baroni, M.8
Cruciani, G.9
-
115
-
-
0031042584
-
A novel method for structure-based prediction of ion channel conductance properties
-
10
-
Smart O.S., Breed J., Smith G.R., Sansom M.S.: A novel method for structure-based prediction of ion channel conductance properties. Biophys. J. 72, 3 (1997), 1109–1126. 10
-
(1997)
Biophys. J.
, vol.72
, Issue.3
, pp. 1109-1126
-
-
Smart, O.S.1
Breed, J.2
Smith, G.R.3
Sansom, M.S.4
-
117
-
-
84910079283
-
Extraction of robust voids and pockets in proteins
-
In, 11, 21
-
Sridharamurthy R., Doraiswamy H., Patel S., Varadarajan R., Natarajan V.: Extraction of robust voids and pockets in proteins. In EuroVis-Short Papers (2013), pp. 67–71. 11, 21
-
(2013)
EuroVis-Short Papers
, pp. 67-71
-
-
Sridharamurthy, R.1
Doraiswamy, H.2
Patel, S.3
Varadarajan, R.4
Natarajan, V.5
-
118
-
-
0027145628
-
The pore dimensions of gramicidin A
-
9
-
Smart O.S., Goodfellow J.M., Wallace B.A.: The pore dimensions of gramicidin A. Biophys. J. 65, 6 (1993), 2455–2460. 9
-
(1993)
Biophys. J.
, vol.65
, Issue.6
, pp. 2455-2460
-
-
Smart, O.S.1
Goodfellow, J.M.2
Wallace, B.A.3
-
119
-
-
84904418519
-
Comparative Visualization of Molecular Surfaces Using Deformable Models
-
18
-
Scharnowski K., Krone M., Reina G., Kulschewski T., Pleiss J., Ertl T.: Comparative Visualization of Molecular Surfaces Using Deformable Models. Comput. Graph. Forum 33, 3 (2014), 191–200. 18
-
(2014)
Comput. Graph. Forum
, vol.33
, Issue.3
, pp. 191-200
-
-
Scharnowski, K.1
Krone, M.2
Reina, G.3
Kulschewski, T.4
Pleiss, J.5
Ertl, T.6
-
120
-
-
0242490780
-
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
-
4
-
Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage B., Amin N., Schwikowski B., Ideker T.: Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Genome Res. 13, 11 (2003), 2498–2504. 4
-
(2003)
Genome Res.
, vol.13
, Issue.11
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, B.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
-
121
-
-
0030404988
-
HOLE: A program for the analysis of the pore dimensions of ion channel structural models
-
9
-
Smart O.S., Neduvelil J.G., Wang X., Wallace B.A., Sansom M. S. P.: HOLE: A program for the analysis of the pore dimensions of ion channel structural models. J. Mol. Graph. 14, 6 (1996), 354–360. 9
-
(1996)
J. Mol. Graph.
, vol.14
, Issue.6
, pp. 354-360
-
-
Smart, O.S.1
Neduvelil, J.G.2
Wang, X.3
Wallace, B.A.4
Sansom, M.S.P.5
-
122
-
-
0030040323
-
Reduced Surface: An Efficient Way to Compute Molecular Surfaces
-
12
-
Sanner M.F., Olson A.J., Spehner J.-C.: Reduced Surface: An Efficient Way to Compute Molecular Surfaces. Biopolymers 38, 3 (1996), 305–320. 12
-
(1996)
Biopolymers
, vol.38
, Issue.3
, pp. 305-320
-
-
Sanner, M.F.1
Olson, A.J.2
Spehner, J.-C.3
-
123
-
-
84884364871
-
MOLE 2.0: advanced approach for analysis of biomacromolecular channels
-
. 9, 21
-
Sehnal B., Svobodová Vařeková R., Berka K., Pravda L., Navrátilová V., Banáš P., Ionescu C.-M., Otyepka M., Koča J.: MOLE 2.0: advanced approach for analysis of biomacromolecular channels. J. Cheminform. 5, 1 (2013). 9, 21
-
(2013)
J. Cheminform.
, vol.5
, pp. 1
-
-
Sehnal, B.1
Svobodová Vařeková, R.2
Berka, K.3
Pravda, L.4
Navrátilová, V.5
Banáš, P.6
Ionescu, C.-M.7
Otyepka, M.8
Koča, J.9
-
124
-
-
84947080780
-
Real-time molecular visualization supporting diffuse interreflections and ambient occlusion
-
18
-
Skanberg R., Vázquez P.-P., Guallar V., Ropinski T.: Real-time molecular visualization supporting diffuse interreflections and ambient occlusion. IEEE Trans. Vis. Comput. Graph. 22, 1 (2016), 718–727. 18
-
(2016)
IEEE Trans. Vis. Comput. Graph.
, vol.22
, Issue.1
, pp. 718-727
-
-
Skanberg, R.1
Vázquez, P.-P.2
Guallar, V.3
Ropinski, T.4
-
125
-
-
0029968922
-
The Contour-Buildup Algorithm to Calculate the Analytical Molecular Surface
-
13
-
Totrov M., Abagyan R.: The Contour-Buildup Algorithm to Calculate the Analytical Molecular Surface. J. Struct. Biol. 116 (1995), 138–143. 13
-
(1995)
J. Struct. Biol.
, vol.116
, pp. 138-143
-
-
Totrov, M.1
Abagyan, R.2
-
126
-
-
33845621535
-
Ambient Occlusion and Edge Cueing for Enhancing Real Time Molecular Visualization
-
17
-
Tarini M., Cignoni P., Montani C.: Ambient Occlusion and Edge Cueing for Enhancing Real Time Molecular Visualization. IEEE Trans. Vis. Comput. Graphics 12, 5 (2006), 1237–1244. 17
-
(2006)
IEEE Trans. Vis. Comput. Graphics
, vol.12
, Issue.5
, pp. 1237-1244
-
-
Tarini, M.1
Cignoni, P.2
Montani, C.3
-
127
-
-
84979858763
-
NPDock: a web server for protein-nucleic acid docking
-
4
-
Tuszynska I., Magnus M., Jonak K., Dawson W., Bujnicki J.M.: NPDock: a web server for protein-nucleic acid docking. Nucleic Acids Res. 43, W1 (2015), W425–W430. 4
-
(2015)
Nucleic Acids Res.
, vol.43
, Issue.W1
, pp. W425-W430
-
-
Tuszynska, I.1
Magnus, M.2
Jonak, K.3
Dawson, W.4
Bujnicki, J.M.5
-
128
-
-
77951214658
-
McVol – A Program for Calculating Protein Volumes and Identifying Cavities by a Monte Carlo Algorithm
-
14, 21
-
Till M., Ullmann G.M.: McVol – A Program for Calculating Protein Volumes and Identifying Cavities by a Monte Carlo Algorithm. J. Mol. Mod. 16, 3 (2010), 419–429. 14, 21
-
(2010)
J. Mol. Mod.
, vol.16
, Issue.3
, pp. 419-429
-
-
Till, M.1
Ullmann, G.M.2
-
129
-
-
77949916296
-
Understanding protein nonfolding
-
4
-
Uversky V.N., Dunker A.K.: Understanding protein nonfolding. BBA Proteins Proteom. 1804, 6 (2010), 1231–1264. 4
-
(2010)
BBA Proteins Proteom.
, vol.1804
, Issue.6
, pp. 1231-1264
-
-
Uversky, V.N.1
Dunker, A.K.2
-
130
-
-
77954262905
-
3V: cavity, channel and cleft volume calculator and extractor
-
13, 14, 21
-
Voss N.R., Gerstein M.: 3V: cavity, channel and cleft volume calculator and extractor. Nucl. Acids Res. 38, suppl 2 (2010), W555–W562. 13, 14, 21
-
(2010)
Nucl. Acids Res.
, vol.38
, pp. W555-W562
-
-
Voss, N.R.1
Gerstein, M.2
-
131
-
-
0024854146
-
A very fast program for visualizing protein surfaces, channels and cavities
-
12
-
Voorintholt R., Kosters M.T., Vegter G., Vriend G., Hol W. G. J.: A very fast program for visualizing protein surfaces, channels and cavities. J. Mol. Graph. 7, 4 (1989), 243–245. 12
-
(1989)
J. Mol. Graph.
, vol.7
, Issue.4
, pp. 243-245
-
-
Voorintholt, R.1
Kosters, M.T.2
Vegter, G.3
Vriend, G.4
Hol, W.G.J.5
-
132
-
-
34547341277
-
PocketPicker: Analysis of Ligand Binding-Sites with Shape Descriptors
-
6, 7, 10, 21
-
Weisel M., Proschak E., Schneider G.: PocketPicker: Analysis of Ligand Binding-Sites with Shape Descriptors. Chem., Cent. J. 1, 1 (2007), 7. 6, 7, 10, 21
-
(2007)
Chem., Cent. J.
, vol.1
, Issue.1
, pp. 7
-
-
Weisel, M.1
Proschak, E.2
Schneider, G.3
-
133
-
-
50849107731
-
MolAxis: Efficient and accurate identification of channels in macromolecules
-
8, 9, 21
-
Yaffe E., Fishelovitch B., Wolfson H.J., Halperin B., Nussinov R.: MolAxis: Efficient and accurate identification of channels in macromolecules. Proteins: Structure, Function, and Bioinformatics 73, 1 (2008), 72–86. 8, 9, 21
-
(2008)
Proteins: Structure, Function, and Bioinformatics
, vol.73
, Issue.1
, pp. 72-86
-
-
Yaffe, E.1
Fishelovitch, B.2
Wolfson, H.J.3
Halperin, B.4
Nussinov, R.5
-
134
-
-
84945897251
-
Ligand tunnels in t. brucei and human cyp51: Insights for parasite-specific drug design
-
Part A (, 4
-
Yu X., Nandekar P., Mustafa G., Cojocaru V., Lepesheva G.I., Wade R.C.: Ligand tunnels in t. brucei and human cyp51: Insights for parasite-specific drug design. Biochim. Biophys. Acta (BBA) – General Subjects 1860, 1, Part A (2016), 67–78. 4
-
(2016)
Biochim. Biophys. Acta (BBA) – General Subjects
, vol.1860
, Issue.1
, pp. 67-78
-
-
Yu, X.1
Nandekar, P.2
Mustafa, G.3
Cojocaru, V.4
Lepesheva, G.I.5
Wade, R.C.6
-
135
-
-
75249088440
-
Roll: A new algorithm for the detection of protein pockets and cavities with a rolling probe sphere
-
13, 14, 21
-
Yu J., Zhou Y., Tanaka I., Yao M.: Roll: A new algorithm for the detection of protein pockets and cavities with a rolling probe sphere. Bioinformatics 26, 1 (2010), 46–52. 13, 14, 21
-
(2010)
Bioinformatics
, vol.26
, Issue.1
, pp. 46-52
-
-
Yu, J.1
Zhou, Y.2
Tanaka, I.3
Yao, M.4
-
136
-
-
79960395595
-
Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction
-
. 21
-
Zhang Z., Li Y., Lin B., Schroeder M., Huang B.: Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction. Bioinformatics (2011). 21
-
(2011)
Bioinformatics
-
-
Zhang, Z.1
Li, Y.2
Lin, B.3
Schroeder, M.4
Huang, B.5
|