-
1
-
-
84871643232
-
A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics
-
Gesing, S.; Grunzke, R.; Krüger, J.; Birkenheuer, G.; Wewior, M.; Schäfer, P.; Schuller, B.; Schuster, J.; Herres-Pawlis, S.; Breuers, S.; Balasko, A.; Kozlovszky, M.; Fabri, A. S.; Packschies, L.; Kacsuk, P.; Blunk, D.; Steinke, T.; Brinkmann, A.; Fels, G.; Müller-Pfefferkorn, R.; Jäkel, R.; Kohlbacher, O. A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics J. Grid Comput. 2012, 10, 769-790
-
(2012)
J. Grid Comput.
, vol.10
, pp. 769-790
-
-
Gesing, S.1
Grunzke, R.2
Krüger, J.3
Birkenheuer, G.4
Wewior, M.5
Schäfer, P.6
Schuller, B.7
Schuster, J.8
Herres-Pawlis, S.9
Breuers, S.10
Balasko, A.11
Kozlovszky, M.12
Fabri, A.S.13
Packschies, L.14
Kacsuk, P.15
Blunk, D.16
Steinke, T.17
Brinkmann, A.18
Fels, G.19
Müller-Pfefferkorn, R.20
Jäkel, R.21
Kohlbacher, O.22
more..
-
2
-
-
84902545391
-
Standards-Based Metadata Management for Molecular Simulations
-
Grunzke, R.; Breuers, S.; Gesing, S.; Herres-Pawlis, S.; Kruse, M.; Blunk, D.; de la Garza, L.; Packschies, L.; Schäfer, P.; Schärfe, C.; Schlemmer, T.; Steinke, T.; Schuller, B.; Müller-Pfefferkorn, R.; Jäkel, R.; Nagel, W. E.; Atkinson, M.; Krüger, J. Standards-Based Metadata Management for Molecular Simulations. Concurr. Comput. Pract. Exp. 2013, http://doi.wiley.com/10.1002/cpe.3116.
-
(2013)
Concurr. Comput. Pract. Exp.
-
-
Grunzke, R.1
Breuers, S.2
Gesing, S.3
Herres-Pawlis, S.4
Kruse, M.5
Blunk, D.6
De La Garza, L.7
Packschies, L.8
Schäfer, P.9
Schärfe, C.10
Schlemmer, T.11
Steinke, T.12
Schuller, B.13
Müller-Pfefferkorn, R.14
Jäkel, R.15
Nagel, W.E.16
Atkinson, M.17
Krüger, J.18
-
3
-
-
0038626673
-
-
Revision C.02.
-
Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, Revision C.02; 2004.
-
(2004)
Gaussian 03
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
Scuseria, G.E.4
Robb, M.A.5
Cheeseman, J.R.6
Montgomery Jr., J.A.7
Vreven, T.8
Kudin, K.N.9
Burant, J.C.10
Millam, J.M.11
Iyengar, S.S.12
Tomasi, J.13
Barone, V.14
Mennucci, B.15
Cossi, M.16
Scalmani, G.17
Rega, N.18
Petersson, G.A.19
Nakatsuji, H.20
Hada, M.21
Ehara, M.22
Toyota, K.23
Fukuda, R.24
Hasegawa, J.25
Ishida, M.26
Nakajima, T.27
Honda, Y.28
Kitao, O.29
Nakai, H.30
Klene, M.31
Li, X.32
Knox, J.E.33
Hratchian, H.P.34
Cross, J.B.35
Bakken, V.36
Adamo, C.37
Jaramillo, J.38
Gomperts, R.39
Stratmann, R.E.40
Yazyev, O.41
Austin, A.J.42
Cammi, R.43
Pomelli, C.44
Ochterski, J.W.45
Ayala, P.Y.46
Morokuma, K.47
Voth, G.A.48
Salvador, P.49
Dannenberg, J.J.50
Zakrzewski, V.G.51
Dapprich, S.52
Daniels, A.D.53
Strain, M.C.54
Farkas, O.55
Malick, D.K.56
Rabuck, A.D.57
Raghavachari, K.58
Foresman, J.B.59
Ortiz, J.V.60
Cui, Q.61
Baboul, A.G.62
Clifford, S.63
Cioslowski, J.64
Stefanov, B.B.65
Liu, G.66
Liashenko, A.67
Piskorz, P.68
Komaromi, I.69
Martin, R.L.70
Fox, D.J.71
Keith, T.72
Al-Laham, M.A.73
Peng, C.Y.74
Nanayakkara, A.75
Challacombe, M.76
Gill, P.M.W.77
Johnson, B.78
Chen, W.79
Wong, M.W.80
Gonzalez, C.81
Pople, J.A.82
more..
-
4
-
-
77955309392
-
NWChem: A Comprehensive and Scalable Open-Source Solution for Large Scale Molecular Simulations
-
Valiev, M.; Bylaska, E. J.; Govind, N.; Kowalski, K.; Straatsma, T. P.; Van Dam, H. J. J.; Wang, D.; Nieplocha, J.; Apra, E.; Windus, T. L.; de Jong, W. A. NWChem: A Comprehensive and Scalable Open-Source Solution for Large Scale Molecular Simulations Comput. Phys. Commun. 2010, 181, 1477-1489
-
(2010)
Comput. Phys. Commun.
, vol.181
, pp. 1477-1489
-
-
Valiev, M.1
Bylaska, E.J.2
Govind, N.3
Kowalski, K.4
Straatsma, T.P.5
Van Dam, H.J.J.6
Wang, D.7
Nieplocha, J.8
Apra, E.9
Windus, T.L.10
De Jong, W.A.11
-
5
-
-
46249092554
-
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
-
Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theory Comput. 2008, 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
-
6
-
-
84902132101
-
CADDSuite - A Workflow-Enabled Suite of Open-Source Tools for Drug Discovery
-
O2+.
-
Kohlbacher, O. CADDSuite-a Workflow-Enabled Suite of Open-Source Tools for Drug Discovery. J. Cheminf. 2012, 4, O2+.
-
(2012)
J. Cheminf.
, vol.4
-
-
Kohlbacher, O.1
-
7
-
-
11644261806
-
Automated Docking Using a Lamarckian Genetic Algorithm and and Empirical Binding Free Energy Function
-
Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated Docking Using a Lamarckian Genetic Algorithm and and Empirical Binding Free Energy Function J. Comput. Chem. 1998, 19, 1639-1662
-
(1998)
J. Comput. Chem.
, vol.19
, pp. 1639-1662
-
-
Morris, G.M.1
Goodsell, D.S.2
Halliday, R.S.3
Huey, R.4
Hart, W.E.5
Belew, R.K.6
Olson, A.J.7
-
8
-
-
0030599010
-
A Fast Flexible Docking Method Using an Incremental Construction Algorithm
-
Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A Fast Flexible Docking Method Using an Incremental Construction Algorithm J. Mol. Biol. 1996, 261, 470-489
-
(1996)
J. Mol. Biol.
, vol.261
, pp. 470-489
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
Klebe, G.4
-
9
-
-
84902207873
-
-
2014 (accessed Apr 5).
-
SCI-BUS. http://www.sci-bus.eu/ (accessed Apr 5, 2014).
-
-
-
-
10
-
-
84902172868
-
-
2014 ER-flow. (accessed Apr 5).
-
ER-flow. https://www.erflow.eu/ (accessed Apr 5, 2014).
-
-
-
-
11
-
-
84902205680
-
-
2014 EDGI. (accessed Apr 5).
-
EDGI. http://edgi-project.eu/ (accessed Apr 5, 2014).
-
-
-
-
12
-
-
84902171971
-
-
2014 WeNMR. (accessed Apr 5).
-
WeNMR. https://www.wenmr.eu/ (accessed Apr 5, 2014).
-
-
-
-
13
-
-
84867367653
-
A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations
-
Van Dijk, M.; Wassenaar, T. A.; Bonvin, A. M. J. J. A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations J. Chem. Theory Comput. 2012, 8, 3463-3472
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 3463-3472
-
-
Van Dijk, M.1
Wassenaar, T.A.2
Bonvin, A.M.J.J.3
-
15
-
-
84860456767
-
MDWeb and MDMoby: An Integrated Web-Based Platform for Molecular Dynamics Simulations
-
Hospital, A.; Andrio, P.; Fenollosa, C.; Cicin-Sain, D.; Orozco, M.; Gelpí, J. L. MDWeb and MDMoby: An Integrated Web-Based Platform for Molecular Dynamics Simulations Bioinformatics 2012, 28, 1278-1279
-
(2012)
Bioinformatics
, vol.28
, pp. 1278-1279
-
-
Hospital, A.1
Andrio, P.2
Fenollosa, C.3
Cicin-Sain, D.4
Orozco, M.5
Gelpí, J.L.6
-
16
-
-
84877662542
-
Molecular Dynamics Science Gateway with Vine Toolkit Providing UNICORE Middleware Support
-
Forschungszentrum Jülich: Toruń, Poland
-
Dziubecki, P.; Grabowski, P.; Kuczynski, T.; Kurowski, K.; Szejnfeld, D.; Tarnawczyk, D.; Wolniewicz, M. Molecular Dynamics Science Gateway with Vine Toolkit Providing UNICORE Middleware Support. In UNICORE Summit 2011: Proceedings, 7-8 July 2011, Toruń, Poland; Forschungszentrum Jülich: Toruń, Poland, 2011; pp 25-34.
-
(2011)
UNICORE Summit 2011: Proceedings, 7 - 8 July 2011, Toruń, Poland
, pp. 25-34
-
-
Dziubecki, P.1
Grabowski, P.2
Kuczynski, T.3
Kurowski, K.4
Szejnfeld, D.5
Tarnawczyk, D.6
Wolniewicz, M.7
-
17
-
-
84902140639
-
AutoDock Gateway for User Friendly Execution of Molecular Docking Simulations in Cloud Systems
-
CRC Press/Taylor & Francis.
-
Farkas, Z.; Kacsuk, P.; Kiss, T.; Borsody, P.; Hajnal, á.; Balaskó, á.; Karóczkai, K. AutoDock Gateway for User Friendly Execution of Molecular Docking Simulations in Cloud Systems. In Cloud Computing with E-science Applications; CRC Press/Taylor & Francis: 2014.
-
(2014)
Cloud Computing with E-science Applications
-
-
Farkas, Z.1
Kacsuk, P.2
Kiss, T.3
Borsody, P.4
Hajnal, Á.5
Balaskó, Á.6
Karóczkai, K.7
-
18
-
-
84856718695
-
An Extension of the Grid Empowered Molecular Simulator to Quantum Reactive Scattering
-
Rampino, S.; Faginas Lago, N.; Laganà, A.; Huarte-Larrañaga, F. An Extension of the Grid Empowered Molecular Simulator to Quantum Reactive Scattering J. Comput. Chem. 2012, 33, 708-714
-
(2012)
J. Comput. Chem.
, vol.33
, pp. 708-714
-
-
Rampino, S.1
Faginas Lago, N.2
Laganà, A.3
Huarte-Larrañaga, F.4
-
19
-
-
78049337966
-
COMPCHEM: Progress Towards GEMS a Grid Empowered Molecular Simulator and beyond
-
Laganà, A.; Costantini, A.; Gervasi, O.; Lago, N. F.; Manuali, C.; Rampino, S. COMPCHEM: Progress Towards GEMS a Grid Empowered Molecular Simulator and Beyond J. Grid Comput. 2010, 8, 571-586
-
(2010)
J. Grid Comput.
, vol.8
, pp. 571-586
-
-
Laganà, A.1
Costantini, A.2
Gervasi, O.3
Lago, N.F.4
Manuali, C.5
Rampino, S.6
-
20
-
-
84902135932
-
-
2014 GridChem. (accessed Apr 5).
-
GridChem. https://www.gridchem.org/ (accessed Apr 5, 2014).
-
-
-
-
21
-
-
33746480261
-
From Proposal to Production: Lessons Learned Developing the Computational Chemistry Grid Cyberinfrastructure
-
Dooley, R.; Milfeld, K.; Guiang, C.; Pamidighantam, S.; Allen, G. From Proposal to Production: Lessons Learned Developing the Computational Chemistry Grid Cyberinfrastructure J. Grid Comput. 2006, 4, 195-208
-
(2006)
J. Grid Comput.
, vol.4
, pp. 195-208
-
-
Dooley, R.1
Milfeld, K.2
Guiang, C.3
Pamidighantam, S.4
Allen, G.5
-
23
-
-
33745949245
-
Workflow-Based Grid Portal for Quantum Mechanics
-
Jin, H. Pan, Y. Xiao, N. Sun, J. Springer: Berlin, Heidelberg
-
Byun, S.-W.; Lee, Y.-K.; Kwon, Y.-W.; Ryu, S.-H.; Jeong, C.-S. Workflow-Based Grid Portal for Quantum Mechanics. In Grid and Cooperative Computing-GCC 2004 Workshops; Jin, H.; Pan, Y.; Xiao, N.; Sun, J., Eds.; Springer: Berlin, Heidelberg, 2004; pp 625-632.
-
(2004)
Grid and Cooperative Computing - GCC 2004 Workshops
, pp. 625-632
-
-
Byun, S.-W.1
Lee, Y.-K.2
Kwon, Y.-W.3
Ryu, S.-H.4
Jeong, C.-S.5
-
24
-
-
0035470282
-
Chemical Markup, XML and the World-Wide Web. 2. Information Objects and the CMLDOM
-
Murray-Rust, P.; Rzepa, H. S. Chemical Markup, XML and the World-Wide Web. 2. Information Objects and the CMLDOM J. Chem. Inf. Comput. Sci. 2001, 41, 1113-1123
-
(2001)
J. Chem. Inf. Comput. Sci.
, vol.41
, pp. 1113-1123
-
-
Murray-Rust, P.1
Rzepa, H.S.2
-
25
-
-
79951728178
-
P-GRADE Portal Family for Grid Infrastructures
-
Kacsuk, P. P-GRADE Portal Family for Grid Infrastructures Concurr. Comput. Pract. Exp. 2011, 23, 235-245
-
(2011)
Concurr. Comput. Pract. Exp.
, vol.23
, pp. 235-245
-
-
Kacsuk, P.1
-
26
-
-
79951855300
-
P-GRADE Portal: A Generic Workflow System to Support User Communities
-
Farkas, Z.; Kacsuk, P. P-GRADE Portal: A Generic Workflow System to Support User Communities Future Gener. Comput. Syst. 2011, 27, 454-465
-
(2011)
Future Gener. Comput. Syst.
, vol.27
, pp. 454-465
-
-
Farkas, Z.1
Kacsuk, P.2
-
27
-
-
84872106344
-
UNICORE 6 - Recent and Future Advancements
-
Streit, A.; Bala, P.; Beck-Ratzka, A.; Benedyczak, K.; Bergmann, S.; Breu, R.; Daivandy, J. M.; Demuth, B.; Eifer, A.; Giesler, A.; Hagemeier, B.; Holl, S.; Huber, V.; Lamla, N.; Mallmann, D.; Memon, A. S.; Memon, M. S.; Rambadt, M.; Riedel, M.; Romberg, M.; Schuller, B.; Schlauch, T.; Schreiber, A.; Soddemann, T.; Ziegler, W. UNICORE 6-Recent and Future Advancements. JUEL-4319; 2010.
-
(2010)
JUEL-4319
-
-
Streit, A.1
Bala, P.2
Beck-Ratzka, A.3
Benedyczak, K.4
Bergmann, S.5
Breu, R.6
Daivandy, J.M.7
Demuth, B.8
Eifer, A.9
Giesler, A.10
Hagemeier, B.11
Holl, S.12
Huber, V.13
Lamla, N.14
Mallmann, D.15
Memon, A.S.16
Memon, M.S.17
Rambadt, M.18
Riedel, M.19
Romberg, M.20
Schuller, B.21
Schlauch, T.22
Schreiber, A.23
Soddemann, T.24
Ziegler, W.25
more..
-
28
-
-
57349095550
-
The XtreemFS Architecture - A Case for Object-Based File Systems in Grids
-
Hupfeld, F.; Cortes, T.; Kolbeck, B.; Stender, J.; Focht, E.; Hess, M.; Malo, J.; Marti, J.; Cesario, E. The XtreemFS Architecture-A Case for Object-Based File Systems in Grids Concurr. Comput. Pract. Exp. 2008, 20, 2049-2060
-
(2008)
Concurr. Comput. Pract. Exp.
, vol.20
, pp. 2049-2060
-
-
Hupfeld, F.1
Cortes, T.2
Kolbeck, B.3
Stender, J.4
Focht, E.5
Hess, M.6
Malo, J.7
Marti, J.8
Cesario, E.9
-
29
-
-
30344452727
-
Globus Toolkit Version 4: Software for Service-Oriented Systems
-
Foster, I. Globus Toolkit Version 4: Software for Service-Oriented Systems IFIP Int. Conf. Netw. Parallel Comput. 2006, Springer-V, 2-13
-
(2006)
IFIP Int. Conf. Netw. Parallel Comput.
, vol.5
, pp. 2-13
-
-
Foster, I.1
-
30
-
-
84902191161
-
-
Internet X.509 Public Key Infrastructure Certificate and Certificate Revocation List (CRL) Profile (RFC 3280). (accessed Apr 5, 2014).
-
Housley, R.; Polk, W.; Ford, W.; Solo, D. Internet X.509 Public Key Infrastructure Certificate and Certificate Revocation List (CRL) Profile (RFC 3280). 2002. http://www.ietf.org/rfc/rfc3280.txt (accessed Apr 5, 2014).
-
(2002)
-
-
Housley, R.1
Polk, W.2
Ford, W.3
Solo, D.4
-
31
-
-
84902132277
-
-
OASIS. SecurityAssertion Markup Language (SAML) V2.0. (. (accessed Apr 5, 2014).
-
OASIS. SecurityAssertion Markup Language (SAML) V2.0. (2002. https://www.oasis-open.org/committees/tc-home.php?wg-abbrev=security (accessed Apr 5, 2014).
-
(2002)
-
-
-
33
-
-
70449679435
-
Striping without Sacrifices: Maintaining POSIX Semantics in a Parallel File System
-
USENIX Association: Berkeley, CA, USA :8
-
Stender, J.; Kolbeck, B.; Hupfeld, F.; Cesario, E.; Focht, E.; Hess, M.; Malo, J.; Martí, J. Striping without Sacrifices: Maintaining POSIX Semantics in a Parallel File System. In First USENIX Workshop on Large-Scale Computing; USENIX Association: Berkeley, CA, USA, 2008; pp 6:1-6:8.
-
(2008)
First USENIX Workshop on Large-Scale Computing
, pp. 61-66
-
-
Stender, J.1
Kolbeck, B.2
Hupfeld, F.3
Cesario, E.4
Focht, E.5
Hess, M.6
Malo, J.7
Martí, J.8
-
34
-
-
84902127416
-
-
2015 Apache Lucene. (accessed Apr 5).
-
Apache Lucene. http://lucene.apache.org/ (accessed Apr 5, 2015).
-
-
-
-
35
-
-
84870472070
-
BioJava: An Open-Source Framework for Bioinformatics in 2012
-
Prlić, A.; Yates, A.; Bliven, S. E.; Rose, P. W.; Jacobsen, J.; Troshin, P. V.; Chapman, M.; Gao, J.; Koh, C. H.; Foisy, S.; Holland, R.; Rimsa, G.; Heuer, M. L.; Brandstätter-Müller, H.; Bourne, P. E.; Willis, S. BioJava: An Open-Source Framework for Bioinformatics in 2012 Bioinformatics 2012, 28, 2693-2695
-
(2012)
Bioinformatics
, vol.28
, pp. 2693-2695
-
-
Prlić, A.1
Yates, A.2
Bliven, S.E.3
Rose, P.W.4
Jacobsen, J.5
Troshin, P.V.6
Chapman, M.7
Gao, J.8
Koh, C.H.9
Foisy, S.10
Holland, R.11
Rimsa, G.12
Heuer, M.L.13
Brandstätter-Müller, H.14
Bourne, P.E.15
Willis, S.16
-
36
-
-
0037361967
-
The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics
-
Steinbeck, C.; Han, Y.; Kuhn, S.; Horlacher, O.; Luttmann, E.; Willighagen, E. The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics J. Chem. Inf. Comput. Sci. 2003, 43, 493-500
-
(2003)
J. Chem. Inf. Comput. Sci.
, vol.43
, pp. 493-500
-
-
Steinbeck, C.1
Han, Y.2
Kuhn, S.3
Horlacher, O.4
Luttmann, E.5
Willighagen, E.6
-
38
-
-
84902167469
-
-
2014 Liferay. (accessed Apr 5).
-
Liferay. https://www.liferay.com/ (accessed Apr 5, 2014).
-
-
-
-
39
-
-
84870683580
-
-
2014 (accessed Apr 5).
-
Grönroos, M. Book of Vaadin. https://vaadin.com/book (accessed Apr 5, 2014).
-
Book of Vaadin
-
-
Grönroos, M.1
-
40
-
-
84902174809
-
-
2014 ChemDoodle. (accessed Apr 5).
-
ChemDoodle. http://www.chemdoodle.com/ (accessed Apr 5, 2014).
-
-
-
-
41
-
-
84902135578
-
-
2014 Dygraphs. (accessed Apr 5).
-
Dygraphs. http://dygraphs.com/ (accessed Apr 5, 2014).
-
-
-
-
42
-
-
0036725277
-
Molecular Dynamics Simulations of Biomolecules
-
Karplus, M.; McCammon, J. A. Molecular Dynamics Simulations of Biomolecules Nat. Struct. Biol. 2002, 9, 646-652
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
43
-
-
80054950510
-
Molecular Dynamics Simulations and Drug Discovery
-
Durrant, J. D.; McCammon, J. A. Molecular Dynamics Simulations and Drug Discovery BMC Biol. 2011, 9, 71
-
(2011)
BMC Biol.
, vol.9
, pp. 71
-
-
Durrant, J.D.1
McCammon, J.A.2
-
44
-
-
34249930405
-
Protein-Folding Dynamics: Overview of Molecular Simulation Techniques
-
Scheraga, H. A.; Khalili, M.; Liwo, A. Protein-Folding Dynamics: Overview of Molecular Simulation Techniques Annu. Rev. Phys. Chem. 2007, 58, 57-83
-
(2007)
Annu. Rev. Phys. Chem.
, vol.58
, pp. 57-83
-
-
Scheraga, H.A.1
Khalili, M.2
Liwo, A.3
-
45
-
-
27344455346
-
Reproducible Polypeptide Folding and Structure Prediction Using Molecular Dynamics Simulations
-
Seibert, M. M.; Patriksson, A.; Hess, B.; van der Spoel, D. Reproducible Polypeptide Folding and Structure Prediction Using Molecular Dynamics Simulations J. Mol. Biol. 2005, 354, 173-183
-
(2005)
J. Mol. Biol.
, vol.354
, pp. 173-183
-
-
Seibert, M.M.1
Patriksson, A.2
Hess, B.3
Van Der Spoel, D.4
-
46
-
-
38049010155
-
Protein Folding Properties from Molecular Dynamics Simulations
-
Kågström, B. Elmroth, E. Dongarra, J. Waśniewski, J. Lecture Notes in Computer Science; Springer: Berlin, Heidelberg, Vol.
-
Spoel, D.; Patriksson, A.; Seibert, M. M. Protein Folding Properties from Molecular Dynamics Simulations. In Applied Parallel Computing. State of the Art in Scientific Computing SE-13; Kågström, B.; Elmroth, E.; Dongarra, J.; Waśniewski, J., Eds.; Lecture Notes in Computer Science; Springer: Berlin, Heidelberg, 2007; Vol. 4699, pp 109-115.
-
(2007)
Applied Parallel Computing. State of the Art in Scientific Computing SE - 13
, vol.4699
, pp. 109-115
-
-
Spoel, D.1
Patriksson, A.2
Seibert, M.M.3
-
47
-
-
84875592758
-
GROMACS 4.5: A High-Throughput and Highly Parallel Open Source Molecular Simulation Toolkit
-
Pronk, S.; Páll, S.; Schulz, R.; Larsson, P.; Bjelkmar, P.; Apostolov, R.; Shirts, M. R.; Smith, J. C.; Kasson, P. M.; van der Spoel, D.; Hess, B.; Lindahl, E. GROMACS 4.5: A High-Throughput and Highly Parallel Open Source Molecular Simulation Toolkit Bioinformatics 2013, 29, 845-854
-
(2013)
Bioinformatics
, vol.29
, pp. 845-854
-
-
Pronk, S.1
Páll, S.2
Schulz, R.3
Larsson, P.4
Bjelkmar, P.5
Apostolov, R.6
Shirts, M.R.7
Smith, J.C.8
Kasson, P.M.9
Van Der Spoel, D.10
Hess, B.11
Lindahl, E.12
-
48
-
-
34548283148
-
Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters
-
IEEE
-
Bowers, K.; Chow, E.; Xu, H.; Dror, R.; Eastwood, M.; Gregersen, B.; Klepeis, J.; Kolossvary, I.; Moraes, M.; Sacerdoti, F.; Salmon, J.; Shan, Y.; Shaw, D. Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters. In ACM/IEEE SC 2006 Conference (SC'06); IEEE: 2006; pp 43-43.
-
(2006)
ACM/IEEE SC 2006 Conference (SC'06)
, pp. 43-43
-
-
Bowers, K.1
Chow, E.2
Xu, H.3
Dror, R.4
Eastwood, M.5
Gregersen, B.6
Klepeis, J.7
Kolossvary, I.8
Moraes, M.9
Sacerdoti, F.10
Salmon, J.11
Shan, Y.12
Shaw, D.13
-
49
-
-
27344436659
-
Scalable Molecular Dynamics with NAMD
-
Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kalé, L.; Schulten, K. Scalable Molecular Dynamics with NAMD J. Comput. Chem. 2005, 26, 1781-1802
-
(2005)
J. Comput. Chem.
, vol.26
, 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
-
50
-
-
84873719639
-
An Overview of the Amber Biomolecular Simulation Package
-
Salomon-Ferrer, R.; Case, D. A.; Walker, R. C. An Overview of the Amber Biomolecular Simulation Package Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2013, 3, 198-210
-
(2013)
Wiley Interdiscip. Rev.: Comput. Mol. Sci.
, vol.3
, pp. 198-210
-
-
Salomon-Ferrer, R.1
Case, D.A.2
Walker, R.C.3
-
51
-
-
4444282928
-
A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation: The GROMOS Force-Field Parameter Sets 53A5 and 53A6
-
Oostenbrink, C.; Villa, A.; Mark, A. E.; van Gunsteren, W. F. A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation: The GROMOS Force-Field Parameter Sets 53A5 and 53A6 J. Comput. Chem. 2004, 25, 1656-1676
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1656-1676
-
-
Oostenbrink, C.1
Villa, A.2
Mark, A.E.3
Van Gunsteren, W.F.4
-
52
-
-
33645941402
-
The OPLS [optimized Potentials for Liquid Simulations] Potential Functions for Proteins, Energy Minimizations for Crystals of Cyclic Peptides and Crambin
-
Jorgensen, W. L.; Tirado-Rives, J. The OPLS [optimized Potentials for Liquid Simulations] Potential Functions for Proteins, Energy Minimizations for Crystals of Cyclic Peptides and Crambin J. Am. Chem. Soc. 1988, 110, 1657-1666
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 1657-1666
-
-
Jorgensen, W.L.1
Tirado-Rives, J.2
-
53
-
-
0041784950
-
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
-
MacKerell, A. D.; Bashford, D.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiórkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins J. Phys. Chem. B 1998, 102, 3586-3616
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
Mackerell, A.D.1
Bashford, D.2
Dunbrack, R.L.3
Evanseck, J.D.4
Field, M.J.5
Fischer, S.6
Gao, J.7
Guo, H.8
Ha, S.9
Joseph-Mccarthy, D.10
Kuchnir, L.11
Kuczera, K.12
Lau, F.T.K.13
Mattos, C.14
Michnick, S.15
Ngo, T.16
Nguyen, D.T.17
Prodhom, B.18
Reiher, W.E.19
Roux, B.20
Schlenkrich, M.21
Smith, J.C.22
Stote, R.23
Straub, J.24
Watanabe, M.25
Wiórkiewicz- Kuczera, J.26
Yin, D.27
Karplus, M.28
more..
-
54
-
-
0242443693
-
Force Fields for Protein Simulations
-
Ponder, J. W.; Case, D. A. Force Fields for Protein Simulations Adv. Protein Chem. 2003, 66, 27-85
-
(2003)
Adv. Protein Chem.
, vol.66
, pp. 27-85
-
-
Ponder, J.W.1
Case, D.A.2
-
55
-
-
0002775934
-
Interaction Models for Water in Relation to Protein Hydration
-
Pullman, B. D. Reidel Publishing Company: Dordrecht
-
Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. Interaction Models for Water in Relation to Protein Hydration. In Intermolecular Forces; Pullman, B., Ed.; D. Reidel Publishing Company: Dordrecht, 1981; pp 331-342.
-
(1981)
Intermolecular Forces
, pp. 331-342
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Hermans, J.4
-
56
-
-
0004016501
-
Comparison of Simple Potential Functions for Simulating Liquid Water
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water J. Chem. Phys. 1983, 79, 926
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
57
-
-
32144446593
-
BALLView: A Tool for Research and Education in Molecular Modeling
-
Moll, A.; Hildebrandt, A.; Lenhof, H.; Kohlbacher, O. BALLView: A Tool for Research and Education in Molecular Modeling Bioinformatics 2006, 365-366
-
(2006)
Bioinformatics
, pp. 365-366
-
-
Moll, A.1
Hildebrandt, A.2
Lenhof, H.3
Kohlbacher, O.4
-
58
-
-
77958140046
-
BALL - Biochemical Algorithms Library 1.3
-
Hildebrandt, A.; Dehof, A. K.; Rurainski, A.; Bertsch, A.; Schumann, M.; Toussaint, N. C.; Moll, A.; Stöckel, D.; Nickels, S.; Mueller, S. C.; Lenhof, H.-P.; Kohlbacher, O. BALL - Biochemical Algorithms Library 1.3 BMC Bioinf. 2010, 11, 531
-
(2010)
BMC Bioinf.
, vol.11
, pp. 531
-
-
Hildebrandt, A.1
Dehof, A.K.2
Rurainski, A.3
Bertsch, A.4
Schumann, M.5
Toussaint, N.C.6
Moll, A.7
Stöckel, D.8
Nickels, S.9
Mueller, S.C.10
Lenhof, H.-P.11
Kohlbacher, O.12
-
59
-
-
84902176220
-
-
2014 XSEDE. (accessed Apr 5).
-
XSEDE. https://www.xsede.org/ (accessed Apr 5, 2014).
-
-
-
-
60
-
-
56649121761
-
TeraGrid Science Gateways and Their Impact on Science
-
IEEE Press: Vol.
-
Wilkins-Diehr, N.; Gannon, D.; Klimeck, G.; Oster, S.; Pamidighantam, S. TeraGrid Science Gateways and Their Impact on Science. IEEE Comput. IEEE Press: 2008; Vol. 41, pp 32-41.
-
(2008)
IEEE Comput.
, vol.41
, pp. 32-41
-
-
Wilkins-Diehr, N.1
Gannon, D.2
Klimeck, G.3
Oster, S.4
Pamidighantam, S.5
-
61
-
-
84902158462
-
Chemomentum - UNICORE 6 Based Infrastructure for Complex Applications in Science and Technology
-
Springer-Verlag: Berlin, Heidelberg
-
Schuller, B.; Demuth, B.; Mix, H.; Rasch, K.; Romberg, M.; Maran, U.; Sild, S.; Bala, P.; del Grosso, E.; Casalegno, M.; Piclin, N.; Pintore, M.; Sudholt, W.; Baldridge, K. K. Chemomentum-UNICORE 6 Based Infrastructure for Complex Applications in Science and Technology. In Euro-Par 2007 Workshops: Parallel Processing (Lecture Notes in Computer Science 4854); Springer-Verlag: Berlin, Heidelberg, 2008; pp 94-103.
-
(2008)
Euro-Par 2007 Workshops: Parallel Processing (Lecture Notes in Computer Science 4854)
, pp. 94-103
-
-
Schuller, B.1
Demuth, B.2
Mix, H.3
Rasch, K.4
Romberg, M.5
Maran, U.6
Sild, S.7
Bala, P.8
Del Grosso, E.9
Casalegno, M.10
Piclin, N.11
Pintore, M.12
Sudholt, W.13
Baldridge, K.K.14
-
62
-
-
33746607287
-
A Scientific Workflow Infrastructure for Computational Chemistry on the Grid
-
Springer-Verlag: Berlin, Heidelberg
-
Sudholt, W.; Altintas, I.; Baldridge, K. K. A Scientific Workflow Infrastructure for Computational Chemistry on the Grid. In Computational Science-ICCS 2006, Lecture Notes in Computer Science 2006; Springer-Verlag: Berlin, Heidelberg, 2006; pp 69-76.
-
(2006)
Computational Science - ICCS 2006, Lecture Notes in Computer Science 2006
, pp. 69-76
-
-
Sudholt, W.1
Altintas, I.2
Baldridge, K.K.3
-
63
-
-
44949236627
-
GEMSTONE: Grid-Enabled Molecular Science through Online Networked Environments
-
Singapore.
-
Baldridge, K. K.; Bhatia, K.; Greenberg, J. P.; Stearn, B.; Mock, S.; Sudholt, W.; Krishnan, S.; Bowne, A.; Amoreira, C.; Potier, Y. GEMSTONE: Grid-Enabled Molecular Science through Online Networked Environments. In Life Sciences Grid Workshop (Satellite of Grid Asia); Singapore, 2005.
-
(2005)
Life Sciences Grid Workshop (Satellite of Grid Asia)
-
-
Baldridge, K.K.1
Bhatia, K.2
Greenberg, J.P.3
Stearn, B.4
Mock, S.5
Sudholt, W.6
Krishnan, S.7
Bowne, A.8
Amoreira, C.9
Potier, Y.10
-
64
-
-
84902212295
-
-
2014 PRACE. (accessed Apr 5).
-
PRACE. http://www.prace-ri.eu/ (accessed Apr 5, 2014).
-
-
-
|