-
1
-
-
0036424666
-
Structural basis of macromolecular recognition
-
J. Janin, S.J. Wodak (Eds.), Protein Modules and Protein-Protein Interaction, Academic Press, Amsterdam
-
S.J. Wodak, J. Janin, Structural basis of macromolecular recognition, in: J. Janin, S.J. Wodak (Eds.), Protein Modules and Protein-Protein Interaction, Volume 61 of Advances in Protein Chemistry, Academic Press, Amsterdam, 2002, pp. 9-73.
-
(2002)
Advances in Protein Chemistry
, vol.61
, pp. 9-73
-
-
Wodak, S.J.1
Janin, J.2
-
2
-
-
0035659985
-
The many faces of Ras: Recognition of small GTP-binding proteins
-
K.D. Corbett, T. Alber, The many faces of Ras: recognition of small GTP-binding proteins, Trends Biochem. Sci. 26 (12) (2001) 710-716.
-
(2001)
Trends Biochem. Sci.
, vol.26
, Issue.12
, pp. 710-716
-
-
Corbett, K.D.1
Alber, T.2
-
3
-
-
0023936327
-
Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure
-
R.L. DesJarlais, R.P. Sheridan, G.L. Seibel, S.J. Dixon, I.D. Kuntz, R. Venkataraghavan, Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure, J. Med. Chem. 31 (4) (1988) 722-729.
-
(1988)
J. Med. Chem.
, vol.31
, Issue.4
, pp. 722-729
-
-
DesJarlais, R.L.1
Sheridan, R.P.2
Seibel, G.L.3
Dixon, S.J.4
Kuntz, I.D.5
Venkataraghavan, R.6
-
4
-
-
0038185277
-
A novel shape complementarity scoring function for protein-protein docking
-
R. Chen, Z. Weng, A novel shape complementarity scoring function for protein-protein docking, Proteins 51 (3) (2003) 397-408.
-
(2003)
Proteins
, vol.51
, Issue.3
, pp. 397-408
-
-
Chen, R.1
Weng, Z.2
-
5
-
-
0037212102
-
Ligandfit: A novel method for the shape-directed rapid docking of ligands to protein active sites
-
C.M. Venkatachalam, X. Jiang, T. Oldfield, M. Waldman, Ligandfit: a novel method for the shape-directed rapid docking of ligands to protein active sites, J. Mol. Gr. Modell. 21 (4) (2003) 289-307.
-
(2003)
J. Mol. Gr. Modell.
, vol.21
, Issue.4
, pp. 289-307
-
-
Venkatachalam, C.M.1
Jiang, X.2
Oldfield, T.3
Waldman, M.4
-
6
-
-
0026567907
-
Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect
-
A. Elisabeth Eriksson, W.A. Baase, X.-J. Zhang, D.W. Heinz, M. Blaber, E.P. Baldwin, B.W. Matthews, Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect, Science 255 (5041) (1992) 178-183.
-
(1992)
Science
, vol.255
, Issue.5041
, pp. 178-183
-
-
Elisabeth Eriksson, A.1
Baase, W.A.2
Zhang, X.-J.3
Heinz, D.W.4
Blaber, M.5
Baldwin, E.P.6
Matthews, B.W.7
-
7
-
-
0025600834
-
Enhanced sampling in molecular dynamics: Use of the time-dependent hartree approximation for a simulation of carbon monoxide diffusion through myoglobin
-
R. Elber, M. Karplus, Enhanced sampling in molecular dynamics: use of the time-dependent hartree approximation for a simulation of carbon monoxide diffusion through myoglobin, J. Am. Chem. Soc. 112 (25) (1990) 9161-9175.
-
(1990)
J. Am. Chem. Soc.
, vol.112
, Issue.25
, pp. 9161-9175
-
-
Elber, R.1
Karplus, M.2
-
8
-
-
77951298113
-
Ligand diffusion in globins: Simulations versus experiment
-
R. Elber, Ligand diffusion in globins: simulations versus experiment, Curr. Opin. Struct. Biol. 20 (2) (2010) 162-167.
-
(2010)
Curr. Opin. Struct. Biol.
, vol.20
, Issue.2
, pp. 162-167
-
-
Elber, R.1
-
9
-
-
3042587451
-
A survey of active site access channels in cytochromes {P450}
-
R.C. Wade, P.J. Winn, I. Schlichting, Sudarko, A survey of active site access channels in cytochromes {P450}, J. Inorg. Biochem. 98 (7) (2004) 1175-1182.
-
(2004)
J. Inorg. Biochem.
, vol.98
, Issue.7
, pp. 1175-1182
-
-
Wade, R.C.1
Winn, P.J.2
Schlichting, I.3
Sudarko4
-
10
-
-
80053107447
-
Active-site hydration and water diffusion in cytochrome p450cam: A highly dynamic process
-
Y. Miao, J. Baudry, Active-site hydration and water diffusion in cytochrome p450cam: a highly dynamic process, Biophys. J. 101 (6) (2011) 1493-1503.
-
(2011)
Biophys. J.
, vol.101
, Issue.6
, pp. 1493-1503
-
-
Miao, Y.1
Baudry, J.2
-
11
-
-
0038546856
-
Trypanosoma cruzi trans-sialidase operates through a covalent sialylenzyme intermediate: Tyrosine is the catalytic nucleophile
-
A.G. Watts, I. Damager, M.L. Amaya, A. Buschiazzo, P. Alzari, A.C. Frasch, S.G. Withers, Trypanosoma cruzi trans-sialidase operates through a covalent sialylenzyme intermediate: tyrosine is the catalytic nucleophile, J. Am. Chem. Soc. 125 (25) (2003) 7532-7533.
-
(2003)
J. Am. Chem. Soc.
, vol.125
, Issue.25
, pp. 7532-7533
-
-
Watts, A.G.1
Damager, I.2
Amaya, M.L.3
Buschiazzo, A.4
Alzari, P.5
Frasch, A.C.6
Withers, S.G.7
-
12
-
-
33750045457
-
Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies
-
S. Liu, J.S. Chang, J.T. Herberg, M.-M. Horng, P.K. Tomich, A.H. Lin, K.R. Marotti, Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies, Proc. Natl. Acad. Sci. U. S. A. 103 (41) (2006) 15178-15183.
-
(2006)
Proc. Natl. Acad. Sci. U. S. A.
, vol.103
, Issue.41
, pp. 15178-15183
-
-
Liu, S.1
Chang, J.S.2
Herberg, J.T.3
Horng, M.-M.4
Tomich, P.K.5
Lin, A.H.6
Marotti, K.R.7
-
13
-
-
0343415156
-
The way things move: Looking under the hood of molecular motor proteins
-
R.D. Vale, R.A. Milligan, The way things move: looking under the hood of molecular motor proteins, Science 288 (5463) (2000) 88-95.
-
(2000)
Science
, vol.288
, Issue.5463
, pp. 88-95
-
-
Vale, R.D.1
Milligan, R.A.2
-
14
-
-
0028607523
-
Cavities and packing at protein interfaces
-
J. Simon, Hubbard, Patrick Argos, Cavities and packing at protein interfaces, Protein Sci. 3 (12) (1994) 2194-2206.
-
(1994)
Protein Sci.
, vol.3
, Issue.12
, pp. 2194-2206
-
-
Hubbard, J.S.1
Argos, P.2
-
15
-
-
52949132638
-
Cavities and atomic packing in protein structures and interfaces
-
Shrihari Sonavane, Pinak Chakrabarti, Cavities and atomic packing in protein structures and interfaces, PLoS Comput. Biol. 4 (9) (2008) e1000188, 09.
-
(2008)
PLoS Comput. Biol.
, vol.4
, Issue.9
-
-
Sonavane, S.1
Chakrabarti, P.2
-
16
-
-
58149333699
-
What induces pocket openings on protein surface patches involved in protein-protein interactions?
-
Susanne Eyrisch, Volkhard Helms, What induces pocket openings on protein surface patches involved in protein-protein interactions? J. Comput. Aided Mol. Des. 23 (2) (2009) 73-86.
-
(2009)
J. Comput. Aided Mol. Des.
, vol.23
, Issue.2
, pp. 73-86
-
-
Eyrisch, S.1
Helms, V.2
-
17
-
-
23244457434
-
Molecular dynamics simulation of sperm whale myoglobin: Effects of mutations and trapped CO on the structure and dynamics of cavities
-
Cecilia Bossa, Andrea Amadei, Isabella Daidone, Massimiliano Anselmi, Beatrice Vallone, Maurizio Brunori, Alfredo Di Nola, Molecular dynamics simulation of sperm whale myoglobin: effects of mutations and trapped CO on the structure and dynamics of cavities, Biophys. J. 89 (1) (2005) 465-474.
-
(2005)
Biophys. J.
, vol.89
, Issue.1
, pp. 465-474
-
-
Bossa, C.1
Amadei, A.2
Daidone, I.3
Anselmi, M.4
Vallone, B.5
Brunori, M.6
Nola, A.D.7
-
18
-
-
48249120004
-
Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin
-
J.Z. Ruscio, D. Kumar, M. Shukla, M.G. Prisant, T.M. Murali, A.V. Onufriev, Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin, Proc. Natl. Acad. Sci. U. S. A. 105 (27) (2008) 9204-9209.
-
(2008)
Proc. Natl. Acad. Sci. U. S. A.
, vol.105
, Issue.27
, pp. 9204-9209
-
-
Ruscio, J.Z.1
Kumar, D.2
Shukla, M.3
Prisant, M.G.4
Murali, T.M.5
Onufriev, A.V.6
-
19
-
-
69049084556
-
Breathing motions of a respiratory protein revealed by molecular dynamics simulations
-
M.A. Scorciapino, A. Robertazzi, M. Casu, P. Ruggerone, M. Ceccarelli, Breathing motions of a respiratory protein revealed by molecular dynamics simulations, J. Am. Chem. Soc. 131 (33) (2009) 11825-11832.
-
(2009)
J. Am. Chem. Soc.
, vol.131
, Issue.33
, pp. 11825-11832
-
-
Scorciapino, M.A.1
Robertazzi, A.2
Casu, M.3
Ruggerone, P.4
Ceccarelli, M.5
-
20
-
-
84871892340
-
CO rebinding kinetics and molecular dynamics simulations highlight dynamic regulation of internal cavities in human cytoglobin
-
M. Gabba, S. Abbruzzetti, F. Spyrakis, F. Forti, S. Bruno, A. Mozzarelli, F. Javier Luque, C. Viappiani, P. Cozzini, M. Nardini, F. Germani, M. Bolognesi, L. Moens, S. Dewilde, CO rebinding kinetics and molecular dynamics simulations highlight dynamic regulation of internal cavities in human cytoglobin, PLOS ONE 8 (1) (2013) e49770, 01.
-
(2013)
PLOS ONE
, vol.8
, Issue.1
-
-
Gabba, M.1
Abbruzzetti, S.2
Spyrakis, F.3
Forti, F.4
Bruno, S.5
Mozzarelli, A.6
Javier Luque, F.7
Viappiani, C.8
Cozzini, P.9
Nardini, M.10
Germani, F.11
Bolognesi, M.12
Moens, L.13
Dewilde, S.14
-
21
-
-
34547583152
-
Transient pockets on protein surfaces involved in protein-protein interaction
-
Susanne Eyrisch, Volkhard Helms, Transient pockets on protein surfaces involved in protein-protein interaction, J. Med. Chem. 50 (15) (2007) 3457-3464.
-
(2007)
J. Med. Chem.
, vol.50
, Issue.15
, pp. 3457-3464
-
-
Eyrisch, S.1
Helms, V.2
-
22
-
-
82255164267
-
MDpocket: Open-source cavity detection and characterization on molecular dynamics trajectories
-
P. Schmidtke, A. Bidon-Chanal, F. Javier Luque, X. Barril, MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories, Bioinformatics 27 (23) (2011) 3276-3285.
-
(2011)
Bioinformatics
, vol.27
, Issue.23
, pp. 3276-3285
-
-
Schmidtke, P.1
Bidon-Chanal, A.2
Javier Luque, F.3
Barril, X.4
-
23
-
-
84860694891
-
Interactive exploration of protein cavities
-
M. Krone, M. Falk, S. Rehm, J. Pleiss, T. Ertl, Interactive exploration of protein cavities, Comput. Gr. Forum 30 (3) (2011) 673-682.
-
(2011)
Comput. Gr. Forum
, vol.30
, Issue.3
, pp. 673-682
-
-
Krone, M.1
Falk, M.2
Rehm, S.3
Pleiss, J.4
Ertl, T.5
-
24
-
-
84857291408
-
Hot spots and transient pockets: Predicting the determinants of small-molecule binding to a protein-protein interface
-
Alexander Metz, Christopher Pfleger, Hannes Kopitz, Stefania Pfeiffer-Marek, Karl-Heinz Baringhaus, Holger Gohlke, Hot spots and transient pockets: predicting the determinants of small-molecule binding to a protein-protein interface, J. Chem. Inf. Model. 52 (1) (2012) 120-133.
-
(2012)
J. Chem. Inf. Model.
, vol.52
, Issue.1
, pp. 120-133
-
-
Metz, A.1
Pfleger, C.2
Kopitz, H.3
Pfeiffer-Marek, S.4
Baringhaus, K.-H.5
Gohlke, H.6
-
25
-
-
84863393146
-
Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets
-
P. Ashford, D. Moss, A. Alex, S. Yeap, A. Povia, I. Nobeli, M. Williams, Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets, BMC Bioinformatics 13 (1) (2012) 39.
-
(2012)
BMC Bioinformatics
, vol.13
, Issue.1
, pp. 39
-
-
Ashford, P.1
Moss, D.2
Alex, A.3
Yeap, S.4
Povia, A.5
Nobeli, I.6
Williams, M.7
-
26
-
-
84878181372
-
TRAPP: A tool for analysis of transient binding pockets in proteins
-
D.B. Kokh, S. Richter, S. Henrich, P. Czodrowski, F. Rippmann, R.C. Wade, TRAPP: a tool for analysis of transient binding pockets in proteins, J. Chem. Inf. Model. 53 (5) (2013) 1235-1252.
-
(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
-
27
-
-
0015222647
-
The interpretation of protein structures: Estimation of static accessibility
-
B. Lee, F.M. Richards, The interpretation of protein structures: estimation of static accessibility, J. Mol. Biol. 55 (3) (1971) 379-400.
-
(1971)
J. Mol. Biol.
, vol.55
, Issue.3
, pp. 379-400
-
-
Lee, B.1
Richards, F.M.2
-
28
-
-
0021107965
-
Solvent-accessible surfaces of proteins and nucleic acids
-
M.L. Connolly, Solvent-accessible surfaces of proteins and nucleic acids, Science 221 (4612) (1983) 709-713.
-
(1983)
Science
, vol.221
, Issue.4612
, pp. 709-713
-
-
Connolly, M.L.1
-
29
-
-
0031687653
-
Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design
-
J. Liang, C. Woodward, C. Woodward, H. Edelsbrunner, H. Edelsbrunner, Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design, Protein Sci. 7 (9) (1998) 1884-1897.
-
(1998)
Protein Sci.
, vol.7
, Issue.9
, pp. 1884-1897
-
-
Liang, J.1
Woodward, C.2
Woodward, C.3
Edelsbrunner, H.4
Edelsbrunner, H.5
-
30
-
-
84874191086
-
Control of substrate access to the active site in methane monooxygenase
-
S.J. Lee, M.S. McCormick, S.J. Lippard, U.-S. Cho, Control of substrate access to the active site in methane monooxygenase, Nature 494 (7437) (2013) 380-384, 02.
-
(2013)
Nature
, vol.494
, Issue.7437
-
-
Lee, S.J.1
McCormick, M.S.2
Lippard, S.J.3
Cho, U.-S.4
-
31
-
-
0030045089
-
Structural and genetic analysis of the folding and function of t4 lysozyme
-
B.W. Matthews, Structural and genetic analysis of the folding and function of t4 lysozyme, FASEB J. 10 (1) (1996) 35-41.
-
(1996)
FASEB J.
, vol.10
, Issue.1
, pp. 35-41
-
-
Matthews, B.W.1
-
32
-
-
0030590215
-
A functional role for protein cavities in domain:Domain motions
-
S.J. Hubbard, P. Argos, A functional role for protein cavities in domain:domain motions, J. Mol. Biol. 261 (2) (1996) 289-300.
-
(1996)
J. Mol. Biol.
, vol.261
, Issue.2
, pp. 289-300
-
-
Hubbard, S.J.1
Argos, P.2
-
33
-
-
1642499388
-
Structure of the dengue virus envelope protein after membrane fusion
-
Y. Modis, S. Ogata, D. Clements, S.C. Harrison, Structure of the dengue virus envelope protein after membrane fusion, Nature 427 (6972) (2004) 313-319.
-
(2004)
Nature
, vol.427
, Issue.6972
, pp. 313-319
-
-
Modis, Y.1
Ogata, S.2
Clements, D.3
Harrison, S.C.4
-
34
-
-
77954913405
-
Use of allostery to identify inhibitors of calmodulin-induced activation of Bacillus anthracis edema factor
-
E. Laine, C. Goncalves, J.C. Karst, A. Lesnard, S. Rault, W.-J. Tang, T.E. Malliavin, D. Ladant, A. Blondel, Use of allostery to identify inhibitors of calmodulin-induced activation of Bacillus anthracis edema factor, Proc. Natl. Acad. Sci. U. S. A. 107 (25) (2010) 11277-11282.
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
, vol.107
, Issue.25
, pp. 11277-11282
-
-
Laine, E.1
Goncalves, C.2
Karst, J.C.3
Lesnard, A.4
Rault, S.5
Tang, W.-J.6
Malliavin, T.E.7
Ladant, D.8
Blondel, A.9
-
35
-
-
0020491251
-
A geometric approach to macromolecule-ligand interactions
-
I.D. Kuntz, J.M. Blaney, S.J. Oatley, R. Langridge, T.E. Ferrin, A geometric approach to macromolecule-ligand interactions, J. Mol. Biol. 161 (2) (1982) 269-288.
-
(1982)
J. Mol. Biol.
, vol.161
, Issue.2
, pp. 269-288
-
-
Kuntz, I.D.1
Blaney, J.M.2
Oatley, S.J.3
Langridge, R.4
Ferrin, T.E.5
-
36
-
-
77955517509
-
Druggable pockets and binding site centric chemical space: A paradigm shift in drug discovery
-
S. Pérot, S. Olivier, M.A. Miteva, A.-C. Camproux, B.O. Villoutreix, Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery, Drug Discov. Today 15 (15-16) (2010) 656-667.
-
(2010)
Drug Discov. Today
, vol.15
, Issue.15-16
, pp. 656-667
-
-
Pérot, S.1
Olivier, S.2
Miteva, M.A.3
Camproux, A.-C.4
Villoutreix, B.O.5
-
37
-
-
63149162777
-
Managing protein flexibility in docking and its applications
-
C. B-Rao, J. Subramanian, S.D. Sharma, Managing protein flexibility in docking and its applications, Drug Discov. Today 14 (7-8) (2009) 394-400.
-
(2009)
Drug Discov. Today
, vol.14
, Issue.7-8
, pp. 394-400
-
-
B-Rao, C.1
Subramanian, J.2
Sharma, S.D.3
-
38
-
-
78149495244
-
Computer-aided drug-discovery techniques that account for receptor flexibility
-
J.D. Durrant, J.A. McCammon, Computer-aided drug-discovery techniques that account for receptor flexibility, Curr. Opin. Pharmacol. 10 (6) (2010) 770-774.
-
(2010)
Curr. Opin. Pharmacol.
, vol.10
, Issue.6
, pp. 770-774
-
-
Durrant, J.D.1
McCammon, J.A.2
-
39
-
-
84879147794
-
Computational identification of a transiently open l1/s3 pocket for reactivation of mutant p53
-
C.D. Wassman, R. Baronio, Ö. Demir, B.D. Wallentine, C.-K. Chen, L.V. Hall, F. Salehi, D.-W. Lin, B.P. Chung, G. Wesley Hatfield, A. Richard Chamberlin, H. Luecke, R.H. Lathrop, P. Kaiser, R.E. Amaro, Computational identification of a transiently open l1/s3 pocket for reactivation of mutant p53, Nat. Commun. 4 (January) (2013) 1407.
-
(2013)
Nat. Commun.
, vol.4
, Issue.JANUARY
, pp. 1407
-
-
Wassman, C.D.1
Baronio, R.2
Demir, Ö.3
Wallentine, B.D.4
Chen, C.-K.5
Hall, L.V.6
Salehi, F.7
Lin, D.-W.8
Chung, B.P.9
Wesley Hatfield, G.10
Richard Chamberlin, A.11
Luecke, H.12
Lathrop, R.H.13
Kaiser, P.14
Amaro, R.E.15
-
40
-
-
49449112578
-
Active site pressurization: A new tool for structure-guided drug design and other studies of protein flexibility
-
I.M. Withers, M.P. Mazanetz, H. Wang, P.M. Fischer, C.A. Laughton, Active site pressurization: a new tool for structure-guided drug design and other studies of protein flexibility, J. Chem. Inf. Model. 48 (7) (2008) 1448-1454.
-
(2008)
J. Chem. Inf. Model.
, vol.48
, Issue.7
, pp. 1448-1454
-
-
Withers, I.M.1
Mazanetz, M.P.2
Wang, H.3
Fischer, P.M.4
Laughton, C.A.5
-
41
-
-
75549087466
-
The flexible pocketome engine for structural chemogenomics
-
E. Jacoby (Ed.), Chemogenomics, Humana Press, Clifton, NJ
-
R. Abagyan, I. Kufareva, The flexible pocketome engine for structural chemogenomics, in: E. Jacoby (Ed.), Chemogenomics, Volume 575 of Methods in Molecular Biology, Humana Press, Clifton, NJ, 2009, pp. 249-279.
-
(2009)
Methods in Molecular Biology
, vol.575
, pp. 249-279
-
-
Abagyan, R.1
Kufareva, I.2
-
42
-
-
47249102090
-
A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)
-
G. Bottegoni, I. Kufareva, M. Totrov, R. Abagyan, A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE), J. Comput. Aided Mol. Des. 22 (5) (2008) 311-325.
-
(2008)
J. Comput. Aided Mol. Des.
, vol.22
, Issue.5
, pp. 311-325
-
-
Bottegoni, G.1
Kufareva, I.2
Totrov, M.3
Abagyan, R.4
-
43
-
-
77951217659
-
Detection of multiscale pockets on protein surfaces using mathematical morphology
-
T. Kawabata, Detection of multiscale pockets on protein surfaces using mathematical morphology, Proteins 78 (5) (2010) 1195-1211.
-
(2010)
Proteins
, vol.78
, Issue.5
, pp. 1195-1211
-
-
Kawabata, T.1
-
44
-
-
0021766921
-
Cavities in proteins: Structure of a metmyoglobin xenon complex solved to 1.9. ang
-
R.F. Tilton, I.D. Kuntz, G.A. Petsko, Cavities in proteins: structure of a metmyoglobin xenon complex solved to 1.9. ang, Biochemistry 23 (13) (1984) 2849-2857.
-
(1984)
Biochemistry
, vol.23
, Issue.13
, pp. 2849-2857
-
-
Tilton, R.F.1
Kuntz, I.D.2
Petsko, G.A.3
-
45
-
-
76149087182
-
Mapping the network of pathways of CO diffusion in myoglobin
-
L. Maragliano, G. Cottone, G. Ciccotti, E. Vanden-Eijnden, Mapping the network of pathways of CO diffusion in myoglobin, J. Am. Chem. Soc. 132 (3) (2010) 1010-1017.
-
(2010)
J. Am. Chem. Soc.
, vol.132
, Issue.3
, pp. 1010-1017
-
-
Maragliano, L.1
Cottone, G.2
Ciccotti, G.3
Vanden-Eijnden, E.4
-
46
-
-
0032802062
-
On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations
-
A. Amadei, M.A. Ceruso, A. Di Nola, On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations, Proteins 36 (4) (1999) 419-424.
-
(1999)
Proteins
, vol.36
, Issue.4
, pp. 419-424
-
-
Amadei, A.1
Ceruso, M.A.2
Di Nola, A.3
-
47
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
J.C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R.D. Skeel, L. Kalé, K. Schulten, Scalable molecular dynamics with NAMD, J. Comput. Chem. 26 (16) (2005) 1781-1802.
-
(2005)
J. Comput. Chem.
, vol.26
, Issue.16
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kalé, L.9
Schulten, K.10
-
48
-
-
67650500988
-
CHARMM: The biomolecular simulation program
-
B.R. Brooks, C.L. Brooks, A.D. Mackerell, L. Nilsson, R.J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A.R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R.W. Pastor, C.B. Post, J.Z. Pu, M. Schaefer, B. Tidor, R.M. Venable, H.L. Woodcock, X. Wu, W. Yang, D.M. York, M. Karplus, CHARMM: the biomolecular simulation program, J. Comput. Chem. 30 (10) (2009) 1545-1614.
-
(2009)
J. Comput. Chem.
, vol.30
, Issue.10
, pp. 1545-1614
-
-
Brooks, B.R.1
Brooks, C.L.2
Mackerell, A.D.3
Nilsson, L.4
Petrella, R.J.5
Roux, B.6
Won, Y.7
Archontis, G.8
Bartels, C.9
Boresch, S.10
Caflisch, A.11
Caves, L.12
Cui, Q.13
Dinner, A.R.14
Feig, M.15
Fischer, S.16
Gao, J.17
Hodoscek, M.18
Im, W.19
Kuczera, K.20
Lazaridis, T.21
Ma, J.22
Ovchinnikov, V.23
Paci, E.24
Pastor, R.W.25
Post, C.B.26
Pu, J.Z.27
Schaefer, M.28
Tidor, B.29
Venable, R.M.30
Woodcock, H.L.31
Wu, X.32
Yang, W.33
York, D.M.34
Karplus, M.35
more..
-
49
-
-
85170282443
-
-
M. Ester, H.-P. Kriegel, Jörg Sander, X. Xu, A density-based algorithm for discovering clusters in large spatial databases with noise KDD, vol. 96, 1996, pp. 226-231.
-
(1996)
A Density-based Algorithm for Discovering Clusters in Large Spatial Databases with Noise KDD
, vol.96
, pp. 226-231
-
-
Ester, M.1
Kriegel, H.-P.2
Sander, J.3
Xu, X.4
-
50
-
-
84897826636
-
Computing cavities, channels, pores and pockets in proteins from non-spherical ligands models
-
L. Benkaidali, F. André, B. Maouche, P. Siregar, M. Benyettou, F. Maurel, M. Petitjean, Computing cavities, channels, pores and pockets in proteins from non-spherical ligands models, Bioinformatics 30 (6) (2014) 792-800.
-
(2014)
Bioinformatics
, vol.30
, Issue.6
, pp. 792-800
-
-
Benkaidali, L.1
André, F.2
Maouche, B.3
Siregar, P.4
Benyettou, M.5
Maurel, F.6
Petitjean, M.7
-
51
-
-
0041353145
-
Structure and mechanism of the lactose permease of Escherichia coli
-
J. Abramson, I. Smirnova, V. Kasho, G. Verner, H. Ronald Kaback, S. Iwata, Structure and mechanism of the lactose permease of Escherichia coli, Science 301 (5633) (2003) 610-615.
-
(2003)
Science
, vol.301
, Issue.5633
, pp. 610-615
-
-
Abramson, J.1
Smirnova, I.2
Kasho, V.3
Verner, G.4
Ronald Kaback, H.5
Iwata, S.6
-
52
-
-
80053056248
-
Opening the periplasmic cavity in lactose permease is the limiting step for sugar binding
-
I. Smirnova, V. Kasho, J. Sugihara, H. Ronald Kaback, Opening the periplasmic cavity in lactose permease is the limiting step for sugar binding, Proc. Natl. Acad. Sci. U. S. A. 108 (37) (2011) 15147-15151.
-
(2011)
Proc. Natl. Acad. Sci. U. S. A.
, vol.108
, Issue.37
, pp. 15147-15151
-
-
Smirnova, I.1
Kasho, V.2
Sugihara, J.3
Ronald Kaback, H.4
-
53
-
-
79959349280
-
Crystal structure of lactose permease in complex with an affinity inactivator yields unique insight into sugar recognition
-
V. Chaptal, S. Kwon, M.R. Sawaya, L. Guan, H. Ronald Kaback, J. Abramson, Crystal structure of lactose permease in complex with an affinity inactivator yields unique insight into sugar recognition, Proc. Natl. Acad. Sci. U. S. A. 108 (23) (2011) 9361-9366.
-
(2011)
Proc. Natl. Acad. Sci. U. S. A.
, vol.108
, Issue.23
, pp. 9361-9366
-
-
Chaptal, V.1
Kwon, S.2
Sawaya, M.R.3
Guan, L.4
Ronald Kaback, H.5
Abramson, J.6
|