-
1
-
-
0024292694
-
The molecular basis of blood coagulation
-
Furie, B. and Furie, B. C. (1988) The molecular basis of blood coagulation Cell 53, 505-518
-
(1988)
Cell
, vol.53
, pp. 505-518
-
-
Furie, B.1
Furie, B.C.2
-
2
-
-
0027304964
-
Structure of Human Des(1-45) Factor-Xa at 2.2-Angstrom Resolution
-
Padmanabhan, K., Padmanabhan, K. P., Tulinsky, A., Park, C. H., Bode, W., Huber, R., Blankenship, D. T., Cardin, A. D., and Kisiel, W. (1993) Structure of Human Des(1-45) Factor-Xa at 2.2-Angstrom Resolution J. Mol. Biol. 232, 947-966
-
(1993)
J. Mol. Biol.
, vol.232
, pp. 947-966
-
-
Padmanabhan, K.1
Padmanabhan, K.P.2
Tulinsky, A.3
Park, C.H.4
Bode, W.5
Huber, R.6
Blankenship, D.T.7
Cardin, A.D.8
Kisiel, W.9
-
3
-
-
33747168208
-
Factor X deficiency: Clinical manifestation of 102 subjects from Europe and Latin America with mutations in the factor 10 gene
-
Herrmann, F. H., Auerswald, G., Ruiz-Saez, A., Navarrete, M., Pollmann, H., Lopaciuk, S., Batorova, A., and Wulff, K. (2006) Factor X deficiency: Clinical manifestation of 102 subjects from Europe and Latin America with mutations in the factor 10 gene Haemophilia 12, 479-489
-
(2006)
Haemophilia
, vol.12
, pp. 479-489
-
-
Herrmann, F.H.1
Auerswald, G.2
Ruiz-Saez, A.3
Navarrete, M.4
Pollmann, H.5
Lopaciuk, S.6
Batorova, A.7
Wulff, K.8
-
4
-
-
0026337077
-
The Coagulation Cascade: Initiation, Maintenance, and Regulation
-
Davie, E. W., Fujikawa, K., and Kisiel, W. (1991) The Coagulation Cascade: Initiation, Maintenance, and Regulation Biochemistry 30, 10363-10370
-
(1991)
Biochemistry
, vol.30
, pp. 10363-10370
-
-
Davie, E.W.1
Fujikawa, K.2
Kisiel, W.3
-
5
-
-
34247224339
-
Theories of blood coagulation
-
Riddel, J. P., Aouizerat, B. E., Miaskowski, C., and Lillicrap, D. P. (2007) Theories of blood coagulation Journal of Pediatric Oncology Nursing 24, 123-131
-
(2007)
Journal of Pediatric Oncology Nursing
, vol.24
, pp. 123-131
-
-
Riddel, J.P.1
Aouizerat, B.E.2
Miaskowski, C.3
Lillicrap, D.P.4
-
6
-
-
0010333946
-
Coagulation factor IXa: The relaxed conformation of Tyr99 blocks substrate binding
-
Hopfner, K. P., Lang, A., Karcher, A., Sichler, K., Kopetzki, E., Brandstetter, H., Huber, R., Bode, W., and Engh, R. A. (1999) Coagulation factor IXa: The relaxed conformation of Tyr99 blocks substrate binding Structure 7, 989-996
-
(1999)
Structure
, vol.7
, pp. 989-996
-
-
Hopfner, K.P.1
Lang, A.2
Karcher, A.3
Sichler, K.4
Kopetzki, E.5
Brandstetter, H.6
Huber, R.7
Bode, W.8
Engh, R.A.9
-
7
-
-
34447333909
-
Cycloalkanediamine derivatives as novel blood coagulation factor Xa inhibitors
-
Nagata, T., Yoshino, T., Haginoya, N., Yoshikawa, K., Isobe, Y., Furugohri, T., and Kanno, H. (2007) Cycloalkanediamine derivatives as novel blood coagulation factor Xa inhibitors Bioorg. Med. Chem. Lett. 17, 4683-4688
-
(2007)
Bioorg. Med. Chem. Lett.
, vol.17
, pp. 4683-4688
-
-
Nagata, T.1
Yoshino, T.2
Haginoya, N.3
Yoshikawa, K.4
Isobe, Y.5
Furugohri, T.6
Kanno, H.7
-
8
-
-
67349271141
-
Design of novel aminopyrrolidine factor Xa inhibitors from a screening hit
-
Zbinden, K. G., Anselm, L., Banner, D. W., Benz, J., Blasco, F., Decoret, G., Himber, J., Kuhn, B., Panday, N., Ricklin, F., Risch, P., Schlatter, D., Stahl, M., Thomi, S., Unger, R., and Haap, W. (2009) Design of novel aminopyrrolidine factor Xa inhibitors from a screening hit Eur. J. Med. Chem. 44, 2787-2795
-
(2009)
Eur. J. Med. Chem.
, vol.44
, pp. 2787-2795
-
-
Zbinden, K.G.1
Anselm, L.2
Banner, D.W.3
Benz, J.4
Blasco, F.5
Decoret, G.6
Himber, J.7
Kuhn, B.8
Panday, N.9
Ricklin, F.10
Risch, P.11
Schlatter, D.12
Stahl, M.13
Thomi, S.14
Unger, R.15
Haap, W.16
-
9
-
-
0036882394
-
Serine protease mechanism and specificity
-
Hedstrom, L. (2002) Serine protease mechanism and specificity Chem. Rev. 102, 4501-4523
-
(2002)
Chem. Rev.
, vol.102
, pp. 4501-4523
-
-
Hedstrom, L.1
-
10
-
-
22244460783
-
Probing the subpockets of factor Xa reveals two binding modes for inhibitors based on a 2-carboxyindole scaffold: A study combining structure-activity relationship and X-ray crystallography
-
Nazare, M., Will, D. W., Matter, H., Schreuder, H., Ritter, K., Urmann, M., Essrich, M., Bauer, A., Wagner, M., Czech, J., Lorenz, M., Laux, V., and Wehner, V. (2005) Probing the subpockets of factor Xa reveals two binding modes for inhibitors based on a 2-carboxyindole scaffold: A study combining structure-activity relationship and X-ray crystallography J. Med. Chem. 48, 4511-4525
-
(2005)
J. Med. Chem.
, vol.48
, pp. 4511-4525
-
-
Nazare, M.1
Will, D.W.2
Matter, H.3
Schreuder, H.4
Ritter, K.5
Urmann, M.6
Essrich, M.7
Bauer, A.8
Wagner, M.9
Czech, J.10
Lorenz, M.11
Laux, V.12
Wehner, V.13
-
11
-
-
84555191616
-
Molecular Recognition at the Active Site of Factor Xa: Cation-π Interactions, Stacking on Planar Peptide Surfaces, and Replacement of Structural Water
-
Salonen, L. M., Holland, M. C., Kaib, P. S. J., Haap, W., Benz, J., Mary, J. L., Kuster, O., Schweizer, W. B., Banner, D. W., and Diederich, F. (2012) Molecular Recognition at the Active Site of Factor Xa: Cation-π Interactions, Stacking on Planar Peptide Surfaces, and Replacement of Structural Water Chem.-Eur. J. 18, 213-222
-
(2012)
Chem.-Eur. J.
, vol.18
, pp. 213-222
-
-
Salonen, L.M.1
Holland, M.C.2
Kaib, P.S.J.3
Haap, W.4
Benz, J.5
Mary, J.L.6
Kuster, O.7
Schweizer, W.B.8
Banner, D.W.9
Diederich, F.10
-
12
-
-
0035004409
-
Perspectives on factor Xa inhibition
-
Rai, R., Sprengeler, P. A., Elrod, K. C., and Young, W. B. (2001) Perspectives on factor Xa inhibition Curr. Med. Chem. 8, 101-119
-
(2001)
Curr. Med. Chem.
, vol.8
, pp. 101-119
-
-
Rai, R.1
Sprengeler, P.A.2
Elrod, K.C.3
Young, W.B.4
-
13
-
-
80051999980
-
Profiling the Structural Determinants for the Selectivity of Representative Factor-Xa and Thrombin Inhibitors Using Combined Ligand-Based and Structure-Based Approaches
-
Bhunia, S. S., Roy, K. K., and Saxena, A. K. (2011) Profiling the Structural Determinants for the Selectivity of Representative Factor-Xa and Thrombin Inhibitors Using Combined Ligand-Based and Structure-Based Approaches J. Chem. Inf. Model. 51, 1966-1985
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 1966-1985
-
-
Bhunia, S.S.1
Roy, K.K.2
Saxena, A.K.3
-
14
-
-
84859085011
-
Progress for Stroke Prevention with Atrial Fibrillation Emergence of Alternative Oral Anticoagulants
-
Katsnelson, M., Sacco, R. L., and Moscucci, M. (2012) Progress for Stroke Prevention with Atrial Fibrillation Emergence of Alternative Oral Anticoagulants Circulation 125, 1577-1583
-
(2012)
Circulation
, vol.125
, pp. 1577-1583
-
-
Katsnelson, M.1
Sacco, R.L.2
Moscucci, M.3
-
15
-
-
84880327613
-
Oral Apixaban for the Treatment of Acute Venous Thromboembolism
-
Investigators A.
-
Agnelli, G., Buller, H. R., Cohen, A., Curto, M., Gallus, A. S., Johnson, M., Masiukiewicz, U., Pak, R., Thompson, J., Raskob, G. E., Weitz, J. I., and Investigators, A. (2013) Oral Apixaban for the Treatment of Acute Venous Thromboembolism N. Engl. J. Med. 369, 799-808
-
(2013)
N. Engl. J. Med.
, vol.369
, pp. 799-808
-
-
Agnelli, G.1
Buller, H.R.2
Cohen, A.3
Curto, M.4
Gallus, A.S.5
Johnson, M.6
Masiukiewicz, U.7
Pak, R.8
Thompson, J.9
Raskob, G.E.10
Weitz, J.I.11
-
16
-
-
84873596181
-
Apixaban for Extended Treatment of Venous Thromboembolism
-
Investigators A.-E.
-
Agnelli, G., Buller, H. R., Cohen, A., Curto, M., Gallus, A. S., Johnson, M., Porcari, A., Raskob, G. E., Weitz, J. I., and Investigators, A.-E. (2013) Apixaban for Extended Treatment of Venous Thromboembolism N. Engl. J. Med. 368, 699-708
-
(2013)
N. Engl. J. Med.
, vol.368
, pp. 699-708
-
-
Agnelli, G.1
Buller, H.R.2
Cohen, A.3
Curto, M.4
Gallus, A.S.5
Johnson, M.6
Porcari, A.7
Raskob, G.E.8
Weitz, J.I.9
-
18
-
-
80755125572
-
A zymogen-like factor Xa variant corrects the coagulation defect in hemophilia
-
Ivanciu, L., Toso, R., Margaritis, P., Pavani, G., Kim, H., Schlachterman, A., Liu, J. H., Clerin, V., Pittman, D. D., Rose-Miranda, R., Shields, K. M., Erbe, D. V., Tobin, J. F., Arruda, V. R., and Camire, R. M. (2011) A zymogen-like factor Xa variant corrects the coagulation defect in hemophilia Nat. Biotechnol. 29, 1028-1033
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 1028-1033
-
-
Ivanciu, L.1
Toso, R.2
Margaritis, P.3
Pavani, G.4
Kim, H.5
Schlachterman, A.6
Liu, J.H.7
Clerin, V.8
Pittman, D.D.9
Rose-Miranda, R.10
Shields, K.M.11
Erbe, D.V.12
Tobin, J.F.13
Arruda, V.R.14
Camire, R.M.15
-
19
-
-
79960424171
-
In vivo genome editing restores haemostasis in a mouse model of haemophilia
-
Li, H. J., Haurigot, V., Doyon, Y., Li, T. J., Wong, S. N. Y., Bhagwat, A. S., Malani, N., Anguela, X. M., Sharma, R., Ivanciu, L., Murphy, S. L., Finn, J. D., Khazi, F. R., Zhou, S. Z., Paschon, D. E., Rebar, E. J., Bushman, F. D., Gregory, P. D., Holmes, M. C., and High, K. A. (2011) In vivo genome editing restores haemostasis in a mouse model of haemophilia Nature 475, 217-221
-
(2011)
Nature
, vol.475
, pp. 217-221
-
-
Li, H.J.1
Haurigot, V.2
Doyon, Y.3
Li, T.J.4
Wong, S.N.Y.5
Bhagwat, A.S.6
Malani, N.7
Anguela, X.M.8
Sharma, R.9
Ivanciu, L.10
Murphy, S.L.11
Finn, J.D.12
Khazi, F.R.13
Zhou, S.Z.14
Paschon, D.E.15
Rebar, E.J.16
Bushman, F.D.17
Gregory, P.D.18
Holmes, M.C.19
High, K.A.20
more..
-
20
-
-
84909624049
-
-
http://www.isth.org/?MutationsRareBleedin.
-
-
-
-
21
-
-
84893915820
-
A recurrent Gly43Asp substitution in coagulation Factor X rigidifies its catalytic pocket and impairs catalytic activity and intracellular trafficking
-
Menegatti, M., Vangone, A., Palla, R., Milano, G., Cavallo, L., Oliva, R., De Cristofaro, R., and Peyvandi, F. (2014) A recurrent Gly43Asp substitution in coagulation Factor X rigidifies its catalytic pocket and impairs catalytic activity and intracellular trafficking Thromb. Res. 133, 481-487
-
(2014)
Thromb. Res.
, vol.133
, pp. 481-487
-
-
Menegatti, M.1
Vangone, A.2
Palla, R.3
Milano, G.4
Cavallo, L.5
Oliva, R.6
De Cristofaro, R.7
Peyvandi, F.8
-
22
-
-
0034696578
-
Substitution of asparagine for arginine 347 of recombinant factor Xa markedly reduces factor Va binding
-
Rudolph, A. E., Porche-Sorbet, R., and Miletich, J. P. (2000) Substitution of asparagine for arginine 347 of recombinant factor Xa markedly reduces factor Va binding Biochemistry 39, 2861-2867
-
(2000)
Biochemistry
, vol.39
, pp. 2861-2867
-
-
Rudolph, A.E.1
Porche-Sorbet, R.2
Miletich, J.P.3
-
23
-
-
2942711324
-
Molecular characterization of factor X deficiency associated with borderline plasma factor X levels
-
Pinotti, M., Monti, M., Boroni, M., Marchetti, G., and Bernardi, F. (2004) Molecular characterization of factor X deficiency associated with borderline plasma factor X levels Haematologica 89, 501-502
-
(2004)
Haematologica
, vol.89
, pp. 501-502
-
-
Pinotti, M.1
Monti, M.2
Boroni, M.3
Marchetti, G.4
Bernardi, F.5
-
24
-
-
12544250870
-
Genetic analysis of hereditary factor X deficiency in a French patient of Sri Lankan ancestry: In vitro expression study indentified Gly366Ser substitution as the molecular basis of the dysfunctional factor X
-
Isshiki, I., Favier, R., Moriki, T., Uchida, T., Ishihara, H., Van Dreden, P., Murata, M., and Ikeda, Y. (2005) Genetic analysis of hereditary factor X deficiency in a French patient of Sri Lankan ancestry: In vitro expression study indentified Gly366Ser substitution as the molecular basis of the dysfunctional factor X Blood Coagulation Fibrinolysis 16, 9-16
-
(2005)
Blood Coagulation Fibrinolysis
, vol.16
, pp. 9-16
-
-
Isshiki, I.1
Favier, R.2
Moriki, T.3
Uchida, T.4
Ishihara, H.5
Van Dreden, P.6
Murata, M.7
Ikeda, Y.8
-
25
-
-
0037330004
-
Impaired prothrombinase activity of factor X Gly381 Asp results in severe familial CRM+ FX deficiency
-
Pinotti, M., Camire, R. M., Baroni, M., Rajab, A., Marchetti, G., and Bernardi, F. (2003) Impaired prothrombinase activity of factor X Gly381 Asp results in severe familial CRM+ FX deficiency Thromb. Haemostasis 89, 243-248
-
(2003)
Thromb. Haemostasis
, vol.89
, pp. 243-248
-
-
Pinotti, M.1
Camire, R.M.2
Baroni, M.3
Rajab, A.4
Marchetti, G.5
Bernardi, F.6
-
26
-
-
0029918581
-
Factor X Stockton: A mild bleeding diathesis associated with an active site mutation in factor X
-
Messier, T. L., Wong, C. Y., Bovill, E. G., Long, G. L., and Church, W. R. (1996) Factor X Stockton: A mild bleeding diathesis associated with an active site mutation in factor X Blood Coagulation Fibrinolysis 7, 5-14
-
(1996)
Blood Coagulation Fibrinolysis
, vol.7
, pp. 5-14
-
-
Messier, T.L.1
Wong, C.Y.2
Bovill, E.G.3
Long, G.L.4
Church, W.R.5
-
27
-
-
18844480017
-
Molecular analysis of the genotype-phenotype relationship in factor X deficiency
-
Millar, D. S., Elliston, L., Deex, P., Krawczak, M., Wacey, A. I., Reynaud, J., Nieuwenhuis, H. K., Bolton-Maggs, P., Mannucci, P. M., Reverter, J. C., Cachia, P., Pasi, K. J., Layton, D. M., and Cooper, D. N. (2000) Molecular analysis of the genotype-phenotype relationship in factor X deficiency Hum. Genet. 106, 249-257
-
(2000)
Hum. Genet.
, vol.106
, pp. 249-257
-
-
Millar, D.S.1
Elliston, L.2
Deex, P.3
Krawczak, M.4
Wacey, A.I.5
Reynaud, J.6
Nieuwenhuis, H.K.7
Bolton-Maggs, P.8
Mannucci, P.M.9
Reverter, J.C.10
Cachia, P.11
Pasi, K.J.12
Layton, D.M.13
Cooper, D.N.14
-
28
-
-
0028231019
-
5 Novel Point Mutations: 2 Causing Hemophilia-B and 3 Causing Factor-X Deficiency
-
Odom, M. W., Leone, G., Destefano, V., Montiel, M. M., Boland, E. J., Anderson, J., and Jagadeeswaran, P. (1994) 5 Novel Point Mutations: 2 Causing Hemophilia-B and 3 Causing Factor-X Deficiency Mol. Cell. Probes 8, 63-65
-
(1994)
Mol. Cell. Probes
, vol.8
, pp. 63-65
-
-
Odom, M.W.1
Leone, G.2
Destefano, V.3
Montiel, M.M.4
Boland, E.J.5
Anderson, J.6
Jagadeeswaran, P.7
-
29
-
-
46249092554
-
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
-
Hess, B., Kutzner, C., van der Spoel, D., and Lindahl, E. (2008) GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4, 435-447
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
Lindahl, E.4
-
30
-
-
77952914469
-
Stabilizing of a Globular Protein by a Highly Complex Water Network: A Molecular Dynamics Simulation Study on Factor Xa
-
Wallnoefer, H. G., Handschuh, S., Liedl, K. R., and Fox, T. (2010) Stabilizing of a Globular Protein by a Highly Complex Water Network: A Molecular Dynamics Simulation Study on Factor Xa J. Phys. Chem. B 114, 7405-7412
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 7405-7412
-
-
Wallnoefer, H.G.1
Handschuh, S.2
Liedl, K.R.3
Fox, T.4
-
31
-
-
0027136282
-
Comparative Protein Modeling by Satisfaction of Spatial Restraints
-
Sali, A. and Blundell, T. L. (1993) Comparative Protein Modeling by Satisfaction of Spatial Restraints J. Mol. Biol. 234, 779-815
-
(1993)
J. Mol. Biol.
, vol.234
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
32
-
-
33748518255
-
Comparison of multiple amber force fields and development of improved protein backbone parameters
-
Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., and Simmerling, C. (2006) Comparison of multiple amber force fields and development of improved protein backbone parameters Proteins 65, 712-725
-
(2006)
Proteins
, vol.65
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
33
-
-
0002271419
-
Computational investigations of protein denaturation: Apomyoglobin and Chaotrope-Arene interactions
-
Jorgensen, W. L., Duffy, E. M., and Tiradorives, J. (1993) Computational investigations of protein denaturation: Apomyoglobin and Chaotrope-Arene interactions Philos. Trans. R. Soc., A 345, 87-96
-
(1993)
Philos. Trans. R. Soc., A
, vol.345
, pp. 87-96
-
-
Jorgensen, W.L.1
Duffy, E.M.2
Tiradorives, J.3
-
34
-
-
33846823909
-
Particle Mesh Ewald: An N.Log(N) Method for Ewald Sums in Large Systems
-
Darden, T., York, D., and Pedersen, L. (1993) Particle Mesh Ewald: An N.Log(N) Method for Ewald Sums in Large Systems J. Chem. Phys. 98, 10089-10092
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
35
-
-
0028697725
-
On the Berendsen Thermostat
-
Lemak, A. S. and Balabaev, N. K. (1994) On the Berendsen Thermostat Mol. Simul. 13, 177-187
-
(1994)
Mol. Simul.
, vol.13
, pp. 177-187
-
-
Lemak, A.S.1
Balabaev, N.K.2
-
36
-
-
0037458399
-
Predicting crystal structures: The Parrinello-Rahman method revisited
-
Martonak, R., Laio, A., and Parrinello, M. (2003) Predicting crystal structures: The Parrinello-Rahman method revisited Phys. Rev. Lett. 90, 1-4
-
(2003)
Phys. Rev. Lett.
, vol.90
, pp. 1-4
-
-
Martonak, R.1
Laio, A.2
Parrinello, M.3
-
37
-
-
80053894476
-
HBonanza: A computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis
-
Durrant, J. D. and McCammon, J. A. (2011) HBonanza: A computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis J. Mol. Graphics Modell. 31, 5-9
-
(2011)
J. Mol. Graphics Modell.
, vol.31
, pp. 5-9
-
-
Durrant, J.D.1
McCammon, J.A.2
-
38
-
-
78649784550
-
Principal component and normal mode analysis of proteins; A quantitative comparison using the GroEL subunit
-
Skjaerven, L., Martinez, A., and Reuter, N. (2011) Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit Proteins 79, 232-243
-
(2011)
Proteins
, vol.79
, pp. 232-243
-
-
Skjaerven, L.1
Martinez, A.2
Reuter, N.3
-
39
-
-
0021449809
-
Quasi-Harmonic Method for Studying Very Low-Frequency Modes in Proteins
-
Levy, R. M., Srinivasan, A. R., Olson, W. K., and Mccammon, J. A. (1984) Quasi-Harmonic Method for Studying Very Low-Frequency Modes in Proteins Biopolymers 23, 1099-1112
-
(1984)
Biopolymers
, vol.23
, pp. 1099-1112
-
-
Levy, R.M.1
Srinivasan, A.R.2
Olson, W.K.3
McCammon, J.A.4
-
40
-
-
0026076090
-
Collective Motions in Proteins: A Covariance Analysis of Atomic Fluctuations in Molecular-Dynamics and Normal Mode Simulations
-
Ichiye, T. and Karplus, M. (1991) Collective Motions in Proteins: A Covariance Analysis of Atomic Fluctuations in Molecular-Dynamics and Normal Mode Simulations Proteins: Struct., Funct., Genet. 11, 205-217
-
(1991)
Proteins: Struct., Funct., Genet.
, vol.11
, pp. 205-217
-
-
Ichiye, T.1
Karplus, M.2
-
41
-
-
0027441950
-
Essential dynamics of proteins
-
Amadei, A., Linssen, A. B. M., and Berendsen, H. J. C. (1993) Essential dynamics of proteins Proteins: Struct., Funct., Genet. 17, 412-425
-
(1993)
Proteins: Struct., Funct., Genet.
, vol.17
, pp. 412-425
-
-
Amadei, A.1
Linssen, A.B.M.2
Berendsen, H.J.C.3
-
42
-
-
79957788878
-
ProDy: Protein Dynamics Inferred from Theory and Experiments
-
Bakan, A., Meireles, L. M., and Bahar, I. (2011) ProDy: Protein Dynamics Inferred from Theory and Experiments Bioinformatics 27, 1575-1577
-
(2011)
Bioinformatics
, vol.27
, pp. 1575-1577
-
-
Bakan, A.1
Meireles, L.M.2
Bahar, I.3
-
43
-
-
0029878720
-
VMD: Visual molecular dynamics
-
Humphrey, W., Dalke, A., and Schulten, K. (1996) VMD: Visual molecular dynamics J. Mol. Graphics Modell. 14, 33-38
-
(1996)
J. Mol. Graphics Modell.
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
44
-
-
82255164267
-
MDpocket: Open-source cavity detection and characterization on molecular dynamics trajectories
-
Schmidtke, P., Bidon-Chanal, A., Luque, F. J., and Barril, X. (2011) MDpocket: Open-source cavity detection and characterization on molecular dynamics trajectories Bioinformatics 27, 3276-3285
-
(2011)
Bioinformatics
, vol.27
, pp. 3276-3285
-
-
Schmidtke, P.1
Bidon-Chanal, A.2
Luque, F.J.3
Barril, X.4
-
45
-
-
77954260902
-
Fpocket: Online tools for protein ensemble pocket detection and tracking
-
Schmidtke, P., Le Guilloux, V., Maupetit, J., and Tuffery, P. (2010) fpocket: Online tools for protein ensemble pocket detection and tracking Nucleic Acids Res. 38, W582-W589
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 582-W589
-
-
Schmidtke, P.1
Le Guilloux, V.2
Maupetit, J.3
Tuffery, P.4
-
46
-
-
84864936006
-
CONS-COCOMAPS: A novel tool to measure and visualize the conservation of inter-residue contacts in multiple docking solutions
-
Vangone, A., Oliva, R., and Cavallo, L. (2012) CONS-COCOMAPS: A novel tool to measure and visualize the conservation of inter-residue contacts in multiple docking solutions BMC Bioinf. 13, 1-9
-
(2012)
BMC Bioinf.
, vol.13
, pp. 1-9
-
-
Vangone, A.1
Oliva, R.2
Cavallo, L.3
-
47
-
-
80053998922
-
COCOMAPS: A web application to analyze and visualize contacts at the interface of biomolecular complexes
-
Vangone, A., Spinelli, R., Scarano, V., Cavallo, L., and Oliva, R. (2011) COCOMAPS: a web application to analyze and visualize contacts at the interface of biomolecular complexes Bioinformatics 27, 2915-2916
-
(2011)
Bioinformatics
, vol.27
, pp. 2915-2916
-
-
Vangone, A.1
Spinelli, R.2
Scarano, V.3
Cavallo, L.4
Oliva, R.5
-
48
-
-
84904961428
-
MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories
-
Abdel-Azeim, S., Chermak, E., Vangone, A., Oliva, R., and Cavallo, L. (2014) MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories BMC Bioinf. 15, 1-11
-
(2014)
BMC Bioinf.
, vol.15
, pp. 1-11
-
-
Abdel-Azeim, S.1
Chermak, E.2
Vangone, A.3
Oliva, R.4
Cavallo, L.5
-
49
-
-
36749006579
-
Docking and scoring protein complexes: CAPRI 3rd edition
-
Lensink, M. F., Mendez, R., and Wodak, S. J. (2007) Docking and scoring protein complexes: CAPRI 3rd edition Proteins 69, 704-718
-
(2007)
Proteins
, vol.69
, pp. 704-718
-
-
Lensink, M.F.1
Mendez, R.2
Wodak, S.J.3
-
50
-
-
84882901819
-
Ranking multiple docking solutions based on the conservation of inter-residue contacts
-
Oliva, R., Vangone, A., and Cavallo, L. (2013) Ranking multiple docking solutions based on the conservation of inter-residue contacts Proteins 81, 1571-1584
-
(2013)
Proteins
, vol.81
, pp. 1571-1584
-
-
Oliva, R.1
Vangone, A.2
Cavallo, L.3
-
51
-
-
84888293717
-
Using a consensus approach based on the conservation of inter-residue contacts to rank CAPRI models
-
Vangone, A., Cavallo, L., and Oliva, R. (2013) Using a consensus approach based on the conservation of inter-residue contacts to rank CAPRI models Proteins 81, 2210-2220
-
(2013)
Proteins
, vol.81
, pp. 2210-2220
-
-
Vangone, A.1
Cavallo, L.2
Oliva, R.3
-
52
-
-
57749191492
-
Principal Component Analysis for Protein Folding Dynamics
-
Maisuradze, G. G., Liwo, A., and Scheraga, H. A. (2009) Principal Component Analysis for Protein Folding Dynamics J. Mol. Biol. 385, 312-329
-
(2009)
J. Mol. Biol.
, vol.385
, pp. 312-329
-
-
Maisuradze, G.G.1
Liwo, A.2
Scheraga, H.A.3
-
53
-
-
84874358394
-
Functionally relevant conformational dynamics of water-soluble proteins
-
Novikov, G. V., Sivozhelezov, V. S., and Shaitan, K. V. (2013) Functionally relevant conformational dynamics of water-soluble proteins Mol. Biol. 47, 149-160
-
(2013)
Mol. Biol.
, vol.47
, pp. 149-160
-
-
Novikov, G.V.1
Sivozhelezov, V.S.2
Shaitan, K.V.3
-
54
-
-
84865965918
-
A dynamic model of long-range conformational adaptations triggered by nucleotide binding in GroEL-GroES
-
Skjaerven, L., Muga, A., Reuter, N., and Martinez, A. (2012) A dynamic model of long-range conformational adaptations triggered by nucleotide binding in GroEL-GroES Proteins 80, 2333-2346
-
(2012)
Proteins
, vol.80
, pp. 2333-2346
-
-
Skjaerven, L.1
Muga, A.2
Reuter, N.3
Martinez, A.4
-
55
-
-
67349196001
-
Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: The myoglobin case
-
Papaleo, E., Mereghetti, P., Fantucci, P., Grandori, R., and De Gioia, L. (2009) Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: The myoglobin case J. Mol. Graphics Modell. 27, 889-899
-
(2009)
J. Mol. Graphics Modell.
, vol.27
, pp. 889-899
-
-
Papaleo, E.1
Mereghetti, P.2
Fantucci, P.3
Grandori, R.4
De Gioia, L.5
-
56
-
-
46249127902
-
Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis
-
Altis, A., Otten, M., Nguyen, P. H., Hegger, R., and Stock, G. (2008) Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis J. Chem. Phys. 128, 245102
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 245102
-
-
Altis, A.1
Otten, M.2
Nguyen, P.H.3
Hegger, R.4
Stock, G.5
-
57
-
-
84894454265
-
The Free Energy Landscape of Pseudorotation in 3′-5′ and 2′-5′ Linked Nucleic Acids
-
Li, L. and Szostak, J. W. (2014) The Free Energy Landscape of Pseudorotation in 3′-5′ and 2′-5′ Linked Nucleic Acids J. Am. Chem. Soc. 136, 2858-2865
-
(2014)
J. Am. Chem. Soc.
, vol.136
, pp. 2858-2865
-
-
Li, L.1
Szostak, J.W.2
-
58
-
-
84886076145
-
Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics
-
Sicard, F. and Senet, P. (2013) Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics J. Chem. Phys. 138, 1-14
-
(2013)
J. Chem. Phys.
, vol.138
, pp. 1-14
-
-
Sicard, F.1
Senet, P.2
-
59
-
-
77950108200
-
Relation between Free Energy Landscapes of Proteins and Dynamics
-
Maisuradze, G. G., Liwo, A., and Scheraga, H. A. (2010) Relation between Free Energy Landscapes of Proteins and Dynamics J. Chem. Theory Comput. 6, 583-595
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 583-595
-
-
Maisuradze, G.G.1
Liwo, A.2
Scheraga, H.A.3
-
60
-
-
84872851728
-
Substrate Recognition and Motion Mode Analyses of PFV Integrase in Complex with Viral DNA via Coarse-Grained Models
-
Hu, J. P., Liu, M., Tang, D. Y., and Chang, S. (2013) Substrate Recognition and Motion Mode Analyses of PFV Integrase in Complex with Viral DNA via Coarse-Grained Models PLoS One 8, e54929
-
(2013)
PLoS One
, vol.8
, pp. 54929
-
-
Hu, J.P.1
Liu, M.2
Tang, D.Y.3
Chang, S.4
-
61
-
-
0032802062
-
On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations
-
Amadei, A., Ceruso, M. A., and Di Nola, A. (1999) On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations Proteins: Struct., Funct., Genet. 36, 419-424
-
(1999)
Proteins: Struct., Funct., Genet.
, vol.36
, pp. 419-424
-
-
Amadei, A.1
Ceruso, M.A.2
Di Nola, A.3
-
62
-
-
33746565283
-
Molecular dynamics of apo-adenylate kinase: A principal component analysis
-
Lou, H. F. and Cukier, R. I. (2006) Molecular dynamics of apo-adenylate kinase: A principal component analysis J. Phys. Chem. B 110, 12796-12808
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 12796-12808
-
-
Lou, H.F.1
Cukier, R.I.2
-
63
-
-
38949218425
-
Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes
-
Yang, L., Song, G., Carriquiry, A., and Jernigan, R. L. (2008) Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes Structure 16, 321-330
-
(2008)
Structure
, vol.16
, pp. 321-330
-
-
Yang, L.1
Song, G.2
Carriquiry, A.3
Jernigan, R.L.4
-
64
-
-
77949382914
-
Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis-application to the HIV-1 protease
-
Batista, P. R., Robert, C. H., Marechal, J. D., Ben Hamida-Rebai, M., Pascutti, P. G., Bisch, P. M., and Perahia, D. (2010) Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis-application to the HIV-1 protease Phys. Chem. Chem. Phys. 12, 2850-2859
-
(2010)
Phys. Chem. Chem. Phys.
, vol.12
, pp. 2850-2859
-
-
Batista, P.R.1
Robert, C.H.2
Marechal, J.D.3
Ben Hamida-Rebai, M.4
Pascutti, P.G.5
Bisch, P.M.6
Perahia, D.7
-
65
-
-
0035044995
-
Conformational change of proteins arising from normal mode calculations
-
Tama, F. and Sanejouand, Y. H. (2001) Conformational change of proteins arising from normal mode calculations Protein Eng. 14, 1-6
-
(2001)
Protein Eng.
, vol.14
, pp. 1-6
-
-
Tama, F.1
Sanejouand, Y.H.2
-
66
-
-
35949003684
-
Role of the α-helix 163-170 in factor Xa catalytic activity
-
Levigne, S., Thiec, F., Cherel, G., Irving, J. A., Fribourg, C., and Christophe, O. D. (2007) Role of the α-helix 163-170 in factor Xa catalytic activity J. Biol. Chem. 282, 31569-31579
-
(2007)
J. Biol. Chem.
, vol.282
, pp. 31569-31579
-
-
Levigne, S.1
Thiec, F.2
Cherel, G.3
Irving, J.A.4
Fribourg, C.5
Christophe, O.D.6
-
67
-
-
58149346050
-
Molecular Dynamics Simulations of Factor Xa: Insight into Conformational Transition of Its Binding Subsites
-
Singh, N. and Briggs, J. M. (2008) Molecular Dynamics Simulations of Factor Xa: Insight into Conformational Transition of Its Binding Subsites Biopolymers 89, 1104-1113
-
(2008)
Biopolymers
, vol.89
, pp. 1104-1113
-
-
Singh, N.1
Briggs, J.M.2
-
68
-
-
84864679050
-
Exploration of conformational transition in the aryl-binding site of human FXa using molecular dynamics simulations
-
Wang, J. F., Hao, P., Li, Y. X., Dai, J. L., and Li, X. (2012) Exploration of conformational transition in the aryl-binding site of human FXa using molecular dynamics simulations J. Mol. Model. 18, 2717-2725
-
(2012)
J. Mol. Model.
, vol.18
, pp. 2717-2725
-
-
Wang, J.F.1
Hao, P.2
Li, Y.X.3
Dai, J.L.4
Li, X.5
-
69
-
-
0033642945
-
Structural stability of binding sites: Consequences for binding affinity and allosteric effects
-
Luque, I. and Freire, E. (2000) Structural stability of binding sites: Consequences for binding affinity and allosteric effects Proteins: Struct., Funct., Genet. Suppl. 4) 63-71
-
(2000)
Proteins: Struct., Funct., Genet.
, pp. 63-71
-
-
Luque, I.1
Freire, E.2
-
70
-
-
27744499156
-
Intrinsic dynamics of an enzyme underlies catalysis
-
Eisenmesser, E. Z., Millet, O., Labeikovsky, W., Korzhnev, D. M., Wolf-Watz, M., Bosco, D. A., Skalicky, J. J., Kay, L. E., and Kern, D. (2005) Intrinsic dynamics of an enzyme underlies catalysis Nature 438, 117-121
-
(2005)
Nature
, vol.438
, pp. 117-121
-
-
Eisenmesser, E.Z.1
Millet, O.2
Labeikovsky, W.3
Korzhnev, D.M.4
Wolf-Watz, M.5
Bosco, D.A.6
Skalicky, J.J.7
Kay, L.E.8
Kern, D.9
|