-
1
-
-
36749113534
-
Generalized Langevin equation approach for atom/solid-surface scattering: general formulation for classical scattering off harmonic solids
-
Adelman S.A., Doll J.D. Generalized Langevin equation approach for atom/solid-surface scattering: general formulation for classical scattering off harmonic solids. The Journal of Chemical Physics 1976, 64:2375-2388.
-
(1976)
The Journal of Chemical Physics
, vol.64
, pp. 2375-2388
-
-
Adelman, S.A.1
Doll, J.D.2
-
4
-
-
0025183708
-
Basic local alignment search tool
-
Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. Journal of Molecular Biology 1990, 215:403-410.
-
(1990)
Journal of Molecular Biology
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
5
-
-
36749107785
-
Molecular dynamics simulations at constant pressure and/or temperature
-
Andersen H.C. Molecular dynamics simulations at constant pressure and/or temperature. The Journal of Chemical Physics 1980, 72:2384-2393.
-
(1980)
The Journal of Chemical Physics
, vol.72
, pp. 2384-2393
-
-
Andersen, H.C.1
-
6
-
-
48749148224
-
Rattle: a velocity version of the shake algorithm for molecular dynamics calculations
-
Andersen H. Rattle: a velocity version of the shake algorithm for molecular dynamics calculations. Journal of Computational Physics 1983, 52:24-34.
-
(1983)
Journal of Computational Physics
, vol.52
, pp. 24-34
-
-
Andersen, H.1
-
7
-
-
0001328298
-
Steepest-descent determination of occupation numbers and energy minimization in the local-density approximation
-
Averill F.W., Painter G.S. Steepest-descent determination of occupation numbers and energy minimization in the local-density approximation. Physical Review B, Condensed Matter 1992, 46:2498-2502.
-
(1992)
Physical Review B, Condensed Matter
, vol.46
, pp. 2498-2502
-
-
Averill, F.W.1
Painter, G.S.2
-
8
-
-
0035747672
-
Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM
-
Bates P.A., Kelley L.A., MacCallum R.M., Sternberg M.J.E. Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM. Proteins: Structure, Function, and Bioinformatics 2001, 45:39-46.
-
(2001)
Proteins: Structure, Function, and Bioinformatics
, vol.45
, pp. 39-46
-
-
Bates, P.A.1
Kelley, L.A.2
MacCallum, R.M.3
Sternberg, M.J.E.4
-
10
-
-
84915763424
-
The amino acid sequence of a protein determines its three-dimensional structure
-
pp. Section 3.6, New York, W.H. Freeman (Ed.)
-
Berg J.M., Tymoczko J.L., Stryer L. The amino acid sequence of a protein determines its three-dimensional structure. Biochemistry 2002, pp. Section 3.6, New York. W.H. Freeman (Ed.).
-
(2002)
Biochemistry
-
-
Berg, J.M.1
Tymoczko, J.L.2
Stryer, L.3
-
11
-
-
0033954256
-
The protein data bank
-
Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The protein data bank. Nucleic Acids Research 2000, 28:235-242.
-
(2000)
Nucleic Acids Research
, vol.28
, 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
-
12
-
-
84857982668
-
The protein data bank at 40: reflecting on the past to prepare for the future
-
Berman HelenÂ.M., Kleywegt GerardÂ.J., Nakamura H., Markley JohnÂ.L. The protein data bank at 40: reflecting on the past to prepare for the future. Structure 2012, 20:391-396.
-
(2012)
Structure
, vol.20
, pp. 391-396
-
-
Berman HelenÂ, M.1
Kleywegt GerardÂ, J.2
Nakamura, H.3
Markley JohnÂ, L.4
-
13
-
-
0017879183
-
The protein data bank: a computer-based archival file for macromolecular structures
-
Bernstein F.C., Koetzle T.F., Williams G.J.B., Meyer E.F., Brice M.D., Rodgers J.R., Kennard O., Shimanouchi T., Tasumi M. The protein data bank: a computer-based archival file for macromolecular structures. Archives of Biochemistry and Biophysics 1978, 185:584-591.
-
(1978)
Archives of Biochemistry and Biophysics
, vol.185
, pp. 584-591
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.B.3
Meyer, E.F.4
Brice, M.D.5
Rodgers, J.R.6
Kennard, O.7
Shimanouchi, T.8
Tasumi, M.9
-
14
-
-
84871539979
-
Current assessment of docking into GPCR crystal structures and homology models: successes, challenges, and guidelines
-
Beuming T., Sherman W. Current assessment of docking into GPCR crystal structures and homology models: successes, challenges, and guidelines. Journal of Chemical Information and Modeling 2012, 52:3263-3277.
-
(2012)
Journal of Chemical Information and Modeling
, vol.52
, pp. 3263-3277
-
-
Beuming, T.1
Sherman, W.2
-
15
-
-
84875862125
-
Critical analysis of the successes and failures of homology models of G protein-coupled receptors
-
Bhattacharya S., Lam A.R., Li H., Balaraman G., Niesen M.J., Vaidehi N. Critical analysis of the successes and failures of homology models of G protein-coupled receptors. Proteins: Structure, Function, and Bioinformatics 2013, 81:729-739.
-
(2013)
Proteins: Structure, Function, and Bioinformatics
, vol.81
, pp. 729-739
-
-
Bhattacharya, S.1
Lam, A.R.2
Li, H.3
Balaraman, G.4
Niesen, M.J.5
Vaidehi, N.6
-
16
-
-
0023305986
-
Knowledge-based prediction of protein structures and the design of novel molecules
-
Blundell T.L., Sibanda B.L., Sternberg M.J.E., Thornton J.M. Knowledge-based prediction of protein structures and the design of novel molecules. Nature 1987, 326:347-352.
-
(1987)
Nature
, vol.326
, pp. 347-352
-
-
Blundell, T.L.1
Sibanda, B.L.2
Sternberg, M.J.E.3
Thornton, J.M.4
-
18
-
-
61449229355
-
Protein structure homology modeling using SWISS-MODEL workspace
-
Bordoli L., Kiefer F., Arnold K., Benkert P., Battey J., Schwede T. Protein structure homology modeling using SWISS-MODEL workspace. Nat. Protocols 2008, 4:1-13.
-
(2008)
Nat. Protocols
, vol.4
, pp. 1-13
-
-
Bordoli, L.1
Kiefer, F.2
Arnold, K.3
Benkert, P.4
Battey, J.5
Schwede, T.6
-
19
-
-
0025830469
-
Amethod to identify protein sequences that fold into a known three-dimensional structure
-
Bowie J.U., Lüthy R., Eisenberg D. Amethod to identify protein sequences that fold into a known three-dimensional structure. Science 1991, 253:164-170.
-
(1991)
Science
, vol.253
, pp. 164-170
-
-
Bowie, J.U.1
Lüthy, R.2
Eisenberg, D.3
-
20
-
-
33751218931
-
Unbinding of retinoic acid from the retinoic acid receptor by random expulsion molecular dynamics
-
Carlsson P., Burendahl S., Nilsson L. Unbinding of retinoic acid from the retinoic acid receptor by random expulsion molecular dynamics. Biophysical Journal 2006, 91:3151-3161.
-
(2006)
Biophysical Journal
, vol.91
, pp. 3151-3161
-
-
Carlsson, P.1
Burendahl, S.2
Nilsson, L.3
-
21
-
-
75349106233
-
Binding sites of the e. Coli DNA recombinase protein to the ssDNA: a computational study
-
Carra C., Cucinotta F.A. Binding sites of the e. Coli DNA recombinase protein to the ssDNA: a computational study. Journal of Biomolecular Structure and Dynamics 2010, 27:407-427.
-
(2010)
Journal of Biomolecular Structure and Dynamics
, vol.27
, pp. 407-427
-
-
Carra, C.1
Cucinotta, F.A.2
-
22
-
-
67649518035
-
Homology modeling in drug discovery: current trends and applications
-
Cavasotto C.N., Phatak S.S. Homology modeling in drug discovery: current trends and applications. Drug Discovery Today 2009, 14:676-683.
-
(2009)
Drug Discovery Today
, vol.14
, pp. 676-683
-
-
Cavasotto, C.N.1
Phatak, S.S.2
-
24
-
-
77952844866
-
Single-molecule pulling simulations can discern active from inactive enzyme inhibitors
-
Colizzi F., Perozzo R., Scapozza L., Recanatini M., Cavalli A. Single-molecule pulling simulations can discern active from inactive enzyme inhibitors. Journal of the American Chemical Society 2010, 132:7361-7371.
-
(2010)
Journal of the American Chemical Society
, vol.132
, pp. 7361-7371
-
-
Colizzi, F.1
Perozzo, R.2
Scapozza, L.3
Recanatini, M.4
Cavalli, A.5
-
25
-
-
0027180507
-
Verification of protein structures: patterns of nonbonded atomic interactions
-
Colovos C., Yeates T.O. Verification of protein structures: patterns of nonbonded atomic interactions. Protein Science 1993, 2:1511-1519.
-
(1993)
Protein Science
, vol.2
, pp. 1511-1519
-
-
Colovos, C.1
Yeates, T.O.2
-
26
-
-
0029011701
-
Asecond generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell W., Cieplak P., Bayly C., Gould I., Merz K., Ferguson D., Spellmeyer D., Fox T., Caldwell J., Kollman P. Asecond generation force field for the simulation of proteins, nucleic acids, and organic molecules. Journal of the American Chemical Society 1995, 117:5179-5197.
-
(1995)
Journal of the American Chemical Society
, vol.117
, pp. 5179-5197
-
-
Cornell, W.1
Cieplak, P.2
Bayly, C.3
Gould, I.4
Merz, K.5
Ferguson, D.6
Spellmeyer, D.7
Fox, T.8
Caldwell, J.9
Kollman, P.10
-
27
-
-
0000673283
-
Deriving the isothermal-isobaric ensemble: the requirement of a 'shell' molecule and applicability to small systems
-
Corti D.S., Soto-Campos G. Deriving the isothermal-isobaric ensemble: the requirement of a 'shell' molecule and applicability to small systems. The Journal of Chemical Physics 1998, 108:7959-7966.
-
(1998)
The Journal of Chemical Physics
, vol.108
, pp. 7959-7966
-
-
Corti, D.S.1
Soto-Campos, G.2
-
28
-
-
36148997683
-
On the calculation of velocity-dependent properties in molecular dynamics simulations using the leapfrog integration algorithm
-
Cuendet M.A., van Gunsteren W.F. On the calculation of velocity-dependent properties in molecular dynamics simulations using the leapfrog integration algorithm. The Journal of Chemical Physics 2007, 127:184102-184108.
-
(2007)
The Journal of Chemical Physics
, vol.127
, pp. 184102-184108
-
-
Cuendet, M.A.1
van Gunsteren, W.F.2
-
29
-
-
34548136236
-
An evaluation of automated homology modelling methods at low target template sequence similarity
-
Dalton J.A.R., Jackson R.M. An evaluation of automated homology modelling methods at low target template sequence similarity. Bioinformatics 2007, 23:1901-1908.
-
(2007)
Bioinformatics
, vol.23
, pp. 1901-1908
-
-
Dalton, J.A.R.1
Jackson, R.M.2
-
30
-
-
33846823909
-
Particle mesh Ewald: an N [center-dot] log (N) method for Ewald sums in large systems
-
Darden T., York D., Pedersen L. Particle mesh Ewald: an N [center-dot] log (N) method for Ewald sums in large systems. The Journal of Chemical Physics 1993, 98:10089-10092.
-
(1993)
The Journal of Chemical Physics
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
32
-
-
68149166660
-
GPCRTree: online hierarchical classification of GPCR function
-
Davies M., Secker A., Halling-Brown M., Moss D., Freitas A., Timmis J., Clark E., Flower D. GPCRTree: online hierarchical classification of GPCR function. BMC Research Notes 2008, 1:67.
-
(2008)
BMC Research Notes
, vol.1
, pp. 67
-
-
Davies, M.1
Secker, A.2
Halling-Brown, M.3
Moss, D.4
Freitas, A.5
Timmis, J.6
Clark, E.7
Flower, D.8
-
33
-
-
80054950510
-
Molecular dynamics simulations and drug discovery
-
Durrant J., McCammon J.A. Molecular dynamics simulations and drug discovery. BMC Biology 2011, 9:71.
-
(2011)
BMC Biology
, vol.9
, pp. 71
-
-
Durrant, J.1
McCammon, J.A.2
-
34
-
-
77953139148
-
On the inhibition of histone deacetylase 8
-
Estiu G., West N., Mazitschek R., Greenberg E., Bradner J.E., Wiest O. On the inhibition of histone deacetylase 8. Bioorganic & Medicinal Chemistry 2010, 18:4103-4110.
-
(2010)
Bioorganic & Medicinal Chemistry
, vol.18
, pp. 4103-4110
-
-
Estiu, G.1
West, N.2
Mazitschek, R.3
Greenberg, E.4
Bradner, J.E.5
Wiest, O.6
-
35
-
-
41149132407
-
Comparative protein structure modeling using MODELLER
-
John Wiley & Sons, Inc
-
Eswar N., Webb B., Marti-Renom M.A., Madhusudhan M.S., Eramian D., Shen M.-y., Pieper U., Sali A. Comparative protein structure modeling using MODELLER. Current Protocols in Protein Science 2001, John Wiley & Sons, Inc.
-
(2001)
Current Protocols in Protein Science
-
-
Eswar, N.1
Webb, B.2
Marti-Renom, M.A.3
Madhusudhan, M.S.4
Eramian, D.5
Shen, M.-Y.6
Pieper, U.7
Sali, A.8
-
36
-
-
41149132407
-
Comparative protein structure modeling using Modeller
-
John Wiley & Sons, Inc
-
Eswar N., Webb B., Marti-Renom M.A., Madhusudhan M.S., Eramian D., Shen M.-y., Pieper U., Sali A. Comparative protein structure modeling using Modeller. Current Protocols in Bioinformatics 2002, John Wiley & Sons, Inc.
-
(2002)
Current Protocols in Bioinformatics
-
-
Eswar, N.1
Webb, B.2
Marti-Renom, M.A.3
Madhusudhan, M.S.4
Eramian, D.5
Shen, M.-Y.6
Pieper, U.7
Sali, A.8
-
37
-
-
13944255377
-
Structure-based drug discovery using GPCR homology Modeling: successful virtual screening for antagonists of the Alpha1A adrenergic receptor
-
Evers A., Klabunde T. Structure-based drug discovery using GPCR homology Modeling: successful virtual screening for antagonists of the Alpha1A adrenergic receptor. Journal of Medicinal Chemistry 2005, 48:1088-1097.
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, pp. 1088-1097
-
-
Evers, A.1
Klabunde, T.2
-
38
-
-
0036720921
-
Completion and refinement of 3-D homology models with restricted molecular dynamics: application to targets 47, 58, and 111 in the CASP modeling competition and posterior analysis
-
Flohil J.A., Vriend G., Berendsen H.J.C. Completion and refinement of 3-D homology models with restricted molecular dynamics: application to targets 47, 58, and 111 in the CASP modeling competition and posterior analysis. Proteins: Structure, Function, and Bioinformatics 2002, 48:593-604.
-
(2002)
Proteins: Structure, Function, and Bioinformatics
, vol.48
, pp. 593-604
-
-
Flohil, J.A.1
Vriend, G.2
Berendsen, H.J.C.3
-
39
-
-
0028309424
-
Adhesion forces between individual ligand-receptor pairs
-
(New York, N.Y.)
-
Florin E.L., Moy V.T., Gaub H.E. Adhesion forces between individual ligand-receptor pairs. Science 1994, 264:415-417. (New York, N.Y.).
-
(1994)
Science
, vol.264
, pp. 415-417
-
-
Florin, E.L.1
Moy, V.T.2
Gaub, H.E.3
-
41
-
-
85040440779
-
Appendix e - integration schemes
-
Academic Press, San Diego
-
Frenkel D., Smit B. Appendix e - integration schemes. Understanding Molecular Simulation 2002, 533-544. Academic Press, San Diego. second ed.
-
(2002)
Understanding Molecular Simulation
, pp. 533-544
-
-
Frenkel, D.1
Smit, B.2
-
43
-
-
0003399724
-
Chapter 4-Molecular dynamics simulations
-
Academic Press, San Diego
-
Frenkel D., Smit B. Chapter 4-Molecular dynamics simulations. Understanding Molecular Simulation 2002, 63-107. Academic Press, San Diego. second ed.
-
(2002)
Understanding Molecular Simulation
, pp. 63-107
-
-
Frenkel, D.1
Smit, B.2
-
44
-
-
0003399724
-
Chapter 6-Molecular dynamics in various ensembles
-
Academic Press, San Diego
-
Frenkel D., Smit B. Chapter 6-Molecular dynamics in various ensembles. Understanding Molecular Simulation 2002, 139-163. Academic Press, San Diego. second ed.
-
(2002)
Understanding Molecular Simulation
, pp. 139-163
-
-
Frenkel, D.1
Smit, B.2
-
45
-
-
22044443487
-
The Newton-Raphson method accelerated by using a line search - comparison between energy functional and residual minimization
-
Fujiwara K., Okamoto Y., Kameari A., Ahagon A. The Newton-Raphson method accelerated by using a line search - comparison between energy functional and residual minimization. Magnetics, IEEE Transactions 2005, 41:1724-1727.
-
(2005)
Magnetics, IEEE Transactions
, vol.41
, pp. 1724-1727
-
-
Fujiwara, K.1
Okamoto, Y.2
Kameari, A.3
Ahagon, A.4
-
46
-
-
0036924186
-
Steered molecular dynamics studies of Titin I1 domain unfolding
-
Gao M., Wilmanns M., Schulten K. Steered molecular dynamics studies of Titin I1 domain unfolding. Biophysical Journal 2002, 83:3435-3445.
-
(2002)
Biophysical Journal
, vol.83
, pp. 3435-3445
-
-
Gao, M.1
Wilmanns, M.2
Schulten, K.3
-
47
-
-
33646002994
-
Comparative modeling for protein structure prediction
-
Ginalski K. Comparative modeling for protein structure prediction. Current Opinion in Structural Biology 2006, 16:172-177.
-
(2006)
Current Opinion in Structural Biology
, vol.16
, pp. 172-177
-
-
Ginalski, K.1
-
48
-
-
36849132539
-
Microcanonical ensemble in quantum statistical mechanics
-
Griffiths R.B. Microcanonical ensemble in quantum statistical mechanics. Journal of Mathematical Physics 1965, 6:1447-1461.
-
(1965)
Journal of Mathematical Physics
, vol.6
, pp. 1447-1461
-
-
Griffiths, R.B.1
-
51
-
-
3843108916
-
Anaphthyridine carboxamide provides evidence for discordant resistance between mechanistically identical inhibitors of HIV-1 integrase
-
Hazuda D.J., Anthony N.J., Gomez R.P., Jolly S.M., Wai J.S., Zhuang L., Fisher T.E., Embrey M., Guare J.P., Egbertson M.S., Vacca J.P., Huff J.R., Felock P.J., Witmer M.V., Stillmock K.A., Danovich R., Grobler J., Miller M.D., Espeseth A.S., Jin L., Chen I.-W., Lin J.H., Kassahun K., Ellis J.D., Wong B.K., Xu W., Pearson P.G., Schleif W.A., Cortese R., Emini E., Summa V., Holloway M.K., Young S.D. Anaphthyridine carboxamide provides evidence for discordant resistance between mechanistically identical inhibitors of HIV-1 integrase. Proceedings of the National Academy of Sciences of the United States of America 2004, 101:11233-11238.
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, pp. 11233-11238
-
-
Hazuda, D.J.1
Anthony, N.J.2
Gomez, R.P.3
Jolly, S.M.4
Wai, J.S.5
Zhuang, L.6
Fisher, T.E.7
Embrey, M.8
Guare, J.P.9
Egbertson, M.S.10
Vacca, J.P.11
Huff, J.R.12
Felock, P.J.13
Witmer, M.V.14
Stillmock, K.A.15
Danovich, R.16
Grobler, J.17
Miller, M.D.18
Espeseth, A.S.19
Jin, L.20
Chen, I.-W.21
Lin, J.H.22
Kassahun, K.23
Ellis, J.D.24
Wong, B.K.25
Xu, W.26
Pearson, P.G.27
Schleif, W.A.28
Cortese, R.29
Emini, E.30
Summa, V.31
Holloway, M.K.32
Young, S.D.33
more..
-
53
-
-
0000388705
-
LINCS: a linear constraint solver for molecular simulations
-
Hess B., Bekker H., Berendsen H., Fraaije J. LINCS: a linear constraint solver for molecular simulations. Journal of Computational Chemistry 1997, 18:1463-1472.
-
(1997)
Journal of Computational Chemistry
, vol.18
, pp. 1463-1472
-
-
Hess, B.1
Bekker, H.2
Berendsen, H.3
Fraaije, J.4
-
54
-
-
0030047142
-
Errors in protein structures
-
Hooft R.W.W., Vriend G., Sander C., Abola E.E. Errors in protein structures. Nature 1996, 381:272.
-
(1996)
Nature
, vol.381
, pp. 272
-
-
Hooft, R.W.W.1
Vriend, G.2
Sander, C.3
Abola, E.E.4
-
55
-
-
79952588669
-
Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations
-
Hou T., Wang J., Li Y., Wang W. Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. Journal of Chemical Information and Modeling 2010, 51:69-82.
-
(2010)
Journal of Chemical Information and Modeling
, vol.51
, pp. 69-82
-
-
Hou, T.1
Wang, J.2
Li, Y.3
Wang, W.4
-
56
-
-
79951996670
-
Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized born surface area methods. II. The accuracy of ranking poses generated from docking
-
Hou T., Wang J., Li Y., Wang W. Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized born surface area methods. II. The accuracy of ranking poses generated from docking. Journal of Computational Chemistry 2011, 32:866-877.
-
(2011)
Journal of Computational Chemistry
, vol.32
, pp. 866-877
-
-
Hou, T.1
Wang, J.2
Li, Y.3
Wang, W.4
-
58
-
-
80052334922
-
Rosetta remodel: a generalized framework for flexible backbone protein design
-
Huang P.-S., Ban Y.-E.A., Richter F., Andre I., Vernon R., Schief W.R., Baker D. Rosetta remodel: a generalized framework for flexible backbone protein design. PLoS One 2011, 6:e24109.
-
(2011)
PLoS One
, vol.6
-
-
Huang, P.-S.1
Ban, Y.-E.A.2
Richter, F.3
Andre, I.4
Vernon, R.5
Schief, W.R.6
Baker, D.7
-
59
-
-
0030987036
-
Molecular dynamics study of unbinding of the avidin-biotin complex
-
Izrailev S., Stepaniants S., Balsera M., Oono Y., Schulten K. Molecular dynamics study of unbinding of the avidin-biotin complex. Biophysical Journal 1997, 72:1568-1581.
-
(1997)
Biophysical Journal
, vol.72
, pp. 1568-1581
-
-
Izrailev, S.1
Stepaniants, S.2
Balsera, M.3
Oono, Y.4
Schulten, K.5
-
60
-
-
0001195575
-
On the determination of molecular fields. Ii. From the equation of state of a gas
-
Jones J.E. On the determination of molecular fields. Ii. From the equation of state of a gas. Proceedings of the Royal Society of London. Series A 1924, 106:463-477.
-
(1924)
Proceedings of the Royal Society of London. Series A
, vol.106
, pp. 463-477
-
-
Jones, J.E.1
-
61
-
-
77956658765
-
Chapter 13 THREADER: protein sequence threading by double dynamic programming
-
Elsevier
-
Jones D., Steven L., Salzberg D.B.S., Simon K. Chapter 13 THREADER: protein sequence threading by double dynamic programming. New Comprehensive Biochemistry 1998, vol 32:285-311. Elsevier.
-
(1998)
New Comprehensive Biochemistry
, vol.32
, pp. 285-311
-
-
Jones, D.1
Steven, L.2
Salzberg, D.B.S.3
Simon, K.4
-
62
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
Jorgensen W.L., Maxwell D.S., Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. Journal of the American Chemical Society 1996, 118:11225-11236.
-
(1996)
Journal of the American Chemical Society
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
63
-
-
80052858265
-
Structure-based drug design to augment hit discovery
-
Kalyaanamoorthy S., Chen Y.-P.P. Structure-based drug design to augment hit discovery. Drug Discovery Today 2011, 16:831-839.
-
(2011)
Drug Discovery Today
, vol.16
, pp. 831-839
-
-
Kalyaanamoorthy, S.1
Chen, Y.-P.P.2
-
64
-
-
84863126869
-
Exploring inhibitor release pathways in histone deacetylases using random acceleration molecular dynamics simulations
-
Kalyaanamoorthy S., Chen Y.-P.P. Exploring inhibitor release pathways in histone deacetylases using random acceleration molecular dynamics simulations. Journal of Chemical Information and Modeling 2012, 52:589-603.
-
(2012)
Journal of Chemical Information and Modeling
, vol.52
, pp. 589-603
-
-
Kalyaanamoorthy, S.1
Chen, Y.-P.P.2
-
66
-
-
84878388412
-
Quantum polarized ligand docking investigation to understand the significance of protonation states in histone deacetylase inhibitors
-
(in press)
-
Kalyaanamoorthy S., Chen Y.-P.P. Quantum polarized ligand docking investigation to understand the significance of protonation states in histone deacetylase inhibitors. Journal of Molecular Graphics and Modelling 2013, (in press).
-
(2013)
Journal of Molecular Graphics and Modelling
-
-
Kalyaanamoorthy, S.1
Chen, Y.-P.P.2
-
67
-
-
0035913529
-
Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on Peptides
-
Kaminski G.A., Friesner R.A., Tirado-Rives J., Jorgensen W.L. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on Peptides. The Journal of Physical Chemistry B 2001, 105:6474-6487.
-
(2001)
The Journal of Physical Chemistry B
, vol.105
, pp. 6474-6487
-
-
Kaminski, G.A.1
Friesner, R.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
68
-
-
70249083714
-
Pathways and mechanisms for product release in the engineered haloalkane dehalogenases explored using classical and random acceleration molecular dynamics simulations
-
Klvana M., Pavlova M., Koudelakova T., Chaloupkova R., Dvorak P., Prokop Z., Stsiapanava A., Kuty M., Kuta-Smatanova I., Dohnalek J., Kulhanek P., Wade R.C., Damborsky J. Pathways and mechanisms for product release in the engineered haloalkane dehalogenases explored using classical and random acceleration molecular dynamics simulations. Journal of Molecular Biology 2009, 392:1339-1356.
-
(2009)
Journal of Molecular Biology
, vol.392
, pp. 1339-1356
-
-
Klvana, M.1
Pavlova, M.2
Koudelakova, T.3
Chaloupkova, R.4
Dvorak, P.5
Prokop, Z.6
Stsiapanava, A.7
Kuty, M.8
Kuta-Smatanova, I.9
Dohnalek, J.10
Kulhanek, P.11
Wade, R.C.12
Damborsky, J.13
-
70
-
-
58149327312
-
An improved method to predict the entropy term with the MM/PBSA approach
-
Kongsted J., Ryde U. An improved method to predict the entropy term with the MM/PBSA approach. Journal of Computer-aided Molecular Design 2009, 23:63-71.
-
(2009)
Journal of Computer-aided Molecular Design
, vol.23
, pp. 63-71
-
-
Kongsted, J.1
Ryde, U.2
-
72
-
-
0032906662
-
Unbinding of retinoic acid from its receptor studied by steered molecular dynamics
-
Kosztin D., Izrailev S., Schulten K. Unbinding of retinoic acid from its receptor studied by steered molecular dynamics. Biophysical Journal 1999, 76:188-197.
-
(1999)
Biophysical Journal
, vol.76
, pp. 188-197
-
-
Kosztin, D.1
Izrailev, S.2
Schulten, K.3
-
73
-
-
34147167680
-
On the relationship between sequence and structure similarities in proteomics
-
Krissinel E. On the relationship between sequence and structure similarities in proteomics. Bioinformatics 2007, 23:717-723.
-
(2007)
Bioinformatics
, vol.23
, pp. 717-723
-
-
Krissinel, E.1
-
74
-
-
84934440741
-
Comparison of protein force fields for molecular dynamics simulations
-
Humana Press
-
Kukol A., Guvench O., MacKerell A. Comparison of protein force fields for molecular dynamics simulations. Molecular Modeling of Proteins 2008, vol. 443:63-88. Humana Press.
-
(2008)
Molecular Modeling of Proteins
, vol.443
, pp. 63-88
-
-
Kukol, A.1
Guvench, O.2
MacKerell, A.3
-
75
-
-
0000243829
-
PROCHECK: a program to check the stereochemical quality of protein structures
-
Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. Journal of Applied Crystallography 1993, 26:283-291.
-
(1993)
Journal of Applied Crystallography
, vol.26
, pp. 283-291
-
-
Laskowski, R.A.1
MacArthur, M.W.2
Moss, D.S.3
Thornton, J.M.4
-
76
-
-
84874522517
-
Towards improved quality of GPCR models by usage of multiple templates and profile-profile comparison
-
Latek D., Pasznik P., Carlomagno T., Filipek S. Towards improved quality of GPCR models by usage of multiple templates and profile-profile comparison. PLoS One 2013, 8:e56742.
-
(2013)
PLoS One
, vol.8
-
-
Latek, D.1
Pasznik, P.2
Carlomagno, T.3
Filipek, S.4
-
79
-
-
84874842514
-
Steered molecular dynamics - a promising tool for drug design
-
Li M.S., Mai B.K. Steered molecular dynamics - a promising tool for drug design. Current Bioinformatics 2012, 7.
-
(2012)
Current Bioinformatics
, vol.7
-
-
Li, M.S.1
Mai, B.K.2
-
80
-
-
78649837413
-
Exploring coumarin egress channels in human cytochrome p450 2a6 by random acceleration and steered molecular dynamics simulations
-
Li W., Shen J., Liu G., Tang Y., Hoshino T. Exploring coumarin egress channels in human cytochrome p450 2a6 by random acceleration and steered molecular dynamics simulations. Proteins: Structure, Function, and Bioinformatics 2011, 79:271-281.
-
(2011)
Proteins: Structure, Function, and Bioinformatics
, vol.79
, pp. 271-281
-
-
Li, W.1
Shen, J.2
Liu, G.3
Tang, Y.4
Hoshino, T.5
-
82
-
-
67650553391
-
Molecular dynamics simulation of ligand dissociation from liver fatty acid binding protein
-
Long D., Mu Y., Yang D. Molecular dynamics simulation of ligand dissociation from liver fatty acid binding protein. PLoS One 2009, 4:e6081.
-
(2009)
PLoS One
, vol.4
-
-
Long, D.1
Mu, Y.2
Yang, D.3
-
83
-
-
0034634393
-
How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms
-
Lüdemann S.K., Lounnas V.R., Wade R.C. How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms. Journal of Molecular Biology 2000, 303:797-811.
-
(2000)
Journal of Molecular Biology
, vol.303
, pp. 797-811
-
-
Lüdemann, S.K.1
Lounnas, V.R.2
Wade, R.C.3
-
84
-
-
0026610767
-
Assessment of protein models with three-dimensional profiles
-
Luthy R., Bowie J.U., Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature 1992, 356:83-85.
-
(1992)
Nature
, vol.356
, pp. 83-85
-
-
Luthy, R.1
Bowie, J.U.2
Eisenberg, D.3
-
85
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
3rkiewicz-Kuczera J., Yin D., Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. The Journal of Physical Chemistry B 1998, 102:3586-3616.
-
(1998)
The Journal of Physical Chemistry B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.D.1
Bashford, D.2
Bellott3
Dunbrack, R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiarkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
86
-
-
79960059801
-
Neuraminidase inhibitor R-125489 - a promising drug for treating influenza virus: steered molecular dynamics approach
-
Mai B.K., Li M.S. Neuraminidase inhibitor R-125489 - a promising drug for treating influenza virus: steered molecular dynamics approach. Biochemical and Biophysical Research Communications 2011, 410:688-691.
-
(2011)
Biochemical and Biophysical Research Communications
, vol.410
, pp. 688-691
-
-
Mai, B.K.1
Li, M.S.2
-
88
-
-
77952003777
-
Homology modeling and docking evaluation of aminergic G protein-coupled receptors
-
McRobb F.M., Capuano B., Crosby I.T., Chalmers D.K., Yuriev E. Homology modeling and docking evaluation of aminergic G protein-coupled receptors. Journal of Chemical Information and Modeling 2010, 50:626-637.
-
(2010)
Journal of Chemical Information and Modeling
, vol.50
, pp. 626-637
-
-
McRobb, F.M.1
Capuano, B.2
Crosby, I.T.3
Chalmers, D.K.4
Yuriev, E.5
-
89
-
-
67349088738
-
Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008
-
Michino M., Abola E., participants G.D., Brooks C.L., Dixon J.S., Moult J., Stevens R.C. Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nature Reviews Drug Discovery 2009, 8:455-463.
-
(2009)
Nature Reviews Drug Discovery
, vol.8
, pp. 455-463
-
-
Michino, M.1
Abola, E.2
Participants, G.D.3
Brooks, C.L.4
Dixon, J.S.5
Moult, J.6
Stevens, R.C.7
-
91
-
-
49449113010
-
The MARTINI coarse-grained force field: extension to proteins
-
Monticelli L., Kandasamy S.K., Periole X., Larson R.G., Tieleman D.P., Marrink S.-J. The MARTINI coarse-grained force field: extension to proteins. Journal of Chemical Theory and Computation 2008, 4:819-834.
-
(2008)
Journal of Chemical Theory and Computation
, vol.4
, pp. 819-834
-
-
Monticelli, L.1
Kandasamy, S.K.2
Periole, X.3
Larson, R.G.4
Tieleman, D.P.5
Marrink, S.-J.6
-
92
-
-
84934436132
-
Classical molecular dynamics in a Nutshell
-
Humana Press
-
Monticelli L., Salonen E., Hug S. Classical molecular dynamics in a Nutshell. Biomolecular Simulations 2013, vol. 924:127-152. Humana Press.
-
(2013)
Biomolecular Simulations
, vol.924
, pp. 127-152
-
-
Monticelli, L.1
Salonen, E.2
Hug, S.3
-
94
-
-
0028961335
-
SCOP: a structural classification of proteins database for the investigation of sequences and structures
-
Murzin A.G., Brenner S.E., Hubbard T., Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. Journal of Molecular Biology 1995, 247:536-540.
-
(1995)
Journal of Molecular Biology
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
95
-
-
84869228349
-
Effect of atomic charge, solvation, entropy, and ligand protonation state on MM-PB(GB)SA binding energies of HIV protease
-
Oehme D.P., Brownlee R.T.C., Wilson D.J.D. Effect of atomic charge, solvation, entropy, and ligand protonation state on MM-PB(GB)SA binding energies of HIV protease. Journal of Computational Chemistry 2012, 33:2566-2580.
-
(2012)
Journal of Computational Chemistry
, vol.33
, pp. 2566-2580
-
-
Oehme, D.P.1
Brownlee, R.T.C.2
Wilson, D.J.D.3
-
96
-
-
33744761830
-
Homology modeling of G-protein-coupled receptors and implications in drug design
-
Patny A., Desai P.V., Avery M.A. Homology modeling of G-protein-coupled receptors and implications in drug design. Current Medicinal Chemistry 2013, 13:1667-1691.
-
(2013)
Current Medicinal Chemistry
, vol.13
, pp. 1667-1691
-
-
Patny, A.1
Desai, P.V.2
Avery, M.A.3
-
97
-
-
70349330482
-
Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate
-
Pavlova M., Klvana M., Prokop Z., Chaloupkova R., Banas P., Otyepka M., Wade R.C., Tsuda M., Nagata Y., Damborsky J. Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate. Nature Chemical Biology 2009, 5:727-733.
-
(2009)
Nature Chemical Biology
, vol.5
, pp. 727-733
-
-
Pavlova, M.1
Klvana, M.2
Prokop, Z.3
Chaloupkova, R.4
Banas, P.5
Otyepka, M.6
Wade, R.C.7
Tsuda, M.8
Nagata, Y.9
Damborsky, J.10
-
98
-
-
0025272240
-
Rapid and sensitive sequence comparison with FASTP and FASTA
-
Academic Press
-
Pearson W.R. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods in Enzymology 1990, vol 183:63-98. Academic Press.
-
(1990)
Methods in Enzymology
, vol.183
, pp. 63-98
-
-
Pearson, W.R.1
-
99
-
-
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. Journal of Computational Chemistry 2005, 26:1781-1802.
-
(2005)
Journal of Computational Chemistry
, 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
-
100
-
-
84862579660
-
Molecular-dynamics simulation of Dioxygen egress from 12/15-lipoxygenase-arachidonic acid complex
-
Pietra F. Molecular-dynamics simulation of Dioxygen egress from 12/15-lipoxygenase-arachidonic acid complex. Chemistry & Biodiversity 2012, 9:1019-1032.
-
(2012)
Chemistry & Biodiversity
, vol.9
, pp. 1019-1032
-
-
Pietra, F.1
-
101
-
-
77957032371
-
Methods for protein homology modelling
-
Elsevier
-
Pitman M.R., Menz R.I., Dilip K., Arora R.M.B., Gautam B.S. Methods for protein homology modelling. Applied Mycology and Biotechnology 2006, vol 6:37-59. Elsevier.
-
(2006)
Applied Mycology and Biotechnology
, vol.6
, pp. 37-59
-
-
Pitman, M.R.1
Menz, R.I.2
Dilip, K.3
Arora, R.M.B.4
Gautam, B.S.5
-
102
-
-
0030598343
-
Deviations from standard atomic volumes as a quality measure for protein crystal structures
-
Pontius J., Richelle J., Wodak S.J. Deviations from standard atomic volumes as a quality measure for protein crystal structures. Journal of Molecular Biology 1996, 264:121-136.
-
(1996)
Journal of Molecular Biology
, vol.264
, pp. 121-136
-
-
Pontius, J.1
Richelle, J.2
Wodak, S.J.3
-
103
-
-
84863098116
-
-
Schrödinger, LLC, New York, NY
-
Prime Version 3.0 2011, Schrödinger, LLC, New York, NY.
-
(2011)
Prime Version 3.0
-
-
-
105
-
-
0013815214
-
Stereochemical criteria for polypeptide and protein chain conformations: II. Allowed conformations for a pair of peptide units
-
Ramakrishnan C., Ramachandran G.N. Stereochemical criteria for polypeptide and protein chain conformations: II. Allowed conformations for a pair of peptide units. Biophysical Journal 1965, 5:909-933.
-
(1965)
Biophysical Journal
, vol.5
, pp. 909-933
-
-
Ramakrishnan, C.1
Ramachandran, G.N.2
-
106
-
-
33645843948
-
Homology modeling of membrane proteins: a critical assessment
-
Reddy C.S., Vijayasarathy K., Srinivas E., Sastry G.M., Sastry G.N. Homology modeling of membrane proteins: a critical assessment. Computational Biology and Chemistry 2006, 30:120-126.
-
(2006)
Computational Biology and Chemistry
, vol.30
, pp. 120-126
-
-
Reddy, C.S.1
Vijayasarathy, K.2
Srinivas, E.3
Sastry, G.M.4
Sastry, G.N.5
-
109
-
-
1842607357
-
Discovery of a novel binding trench in HIV integrase
-
Schames J.R., Henchman R.H., Siegel J.S., Sotriffer C.A., Ni H., McCammon J.A. Discovery of a novel binding trench in HIV integrase. Journal of Medicinal Chemistry 2004, 47:1879-1881.
-
(2004)
Journal of Medicinal Chemistry
, vol.47
, pp. 1879-1881
-
-
Schames, J.R.1
Henchman, R.H.2
Siegel, J.S.3
Sotriffer, C.A.4
Ni, H.5
McCammon, J.A.6
-
110
-
-
8844227448
-
Mutant G-protein-coupled receptors as a cause of human diseases
-
Schöneberg T., Schulz A., Biebermann H., Hermsdorf T., Römpler H., Sangkuhl K. Mutant G-protein-coupled receptors as a cause of human diseases. Pharmacology & Therapeutics 2004, 104:173-206.
-
(2004)
Pharmacology & Therapeutics
, vol.104
, pp. 173-206
-
-
Schöneberg, T.1
Schulz, A.2
Biebermann, H.3
Hermsdorf, T.4
Römpler, H.5
Sangkuhl, K.6
-
111
-
-
0042622380
-
SWISS-MODEL: an automated protein homology-modeling server
-
Schwede T., Kopp J., Guex N., Peitsch M.C. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Research 2003, 31:3381-3385.
-
(2003)
Nucleic Acids Research
, vol.31
, pp. 3381-3385
-
-
Schwede, T.1
Kopp, J.2
Guex, N.3
Peitsch, M.C.4
-
112
-
-
84863348961
-
Investigation of indazole unbinding pathways in CYP2E1 by Molecular dynamics simulations
-
Shen Z., Cheng F., Xu Y., Fu J., Xiao W., Shen J., Liu G., Li W., Tang Y. Investigation of indazole unbinding pathways in CYP2E1 by Molecular dynamics simulations. PLoS One 2012, 7:e33500.
-
(2012)
PLoS One
, vol.7
-
-
Shen, Z.1
Cheng, F.2
Xu, Y.3
Fu, J.4
Xiao, W.5
Shen, J.6
Liu, G.7
Li, W.8
Tang, Y.9
-
113
-
-
33750474069
-
Periodic boundary condition induced breakdown of the equipartition principle and other kinetic effects of finite sample size in classical hard-sphere molecular dynamics simulation
-
Shirts R.B., Burt S.R., Johnson A.M. Periodic boundary condition induced breakdown of the equipartition principle and other kinetic effects of finite sample size in classical hard-sphere molecular dynamics simulation. The Journal of Chemical Physics 2006, 125:164102-164109.
-
(2006)
The Journal of Chemical Physics
, vol.125
, pp. 164102-164109
-
-
Shirts, R.B.1
Burt, S.R.2
Johnson, A.M.3
-
114
-
-
0027490731
-
Recognition of errors in three-dimensional structures of proteins
-
Sippl M.J. Recognition of errors in three-dimensional structures of proteins. Proteins: Structure, Function, and Bioinformatics 1993, 17:355-362.
-
(1993)
Proteins: Structure, Function, and Bioinformatics
, vol.17
, pp. 355-362
-
-
Sippl, M.J.1
-
115
-
-
32844457567
-
Accurate calculation of hydration free energies using macroscopic solvent models
-
Sitkoff D., Sharp K.A., Honig B. Accurate calculation of hydration free energies using macroscopic solvent models. The Journal of Physical Chemistry 1994, 98:1978-1988.
-
(1994)
The Journal of Physical Chemistry
, vol.98
, pp. 1978-1988
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
116
-
-
34249930159
-
Single-molecule experiments invitro and in silico
-
Sotomayor M., Schulten K. Single-molecule experiments invitro and in silico. Science 2007, 316:1144-1148.
-
(2007)
Science
, vol.316
, pp. 1144-1148
-
-
Sotomayor, M.1
Schulten, K.2
-
117
-
-
0000179199
-
Knowledge based modelling of homologous proteins, part II: rules for the conformations of substituted sidechains
-
Sutcliffe M.J., Hayes F.R.F., Blundell T.L. Knowledge based modelling of homologous proteins, part II: rules for the conformations of substituted sidechains. Protein Engineering 1987, 1:385-392.
-
(1987)
Protein Engineering
, vol.1
, pp. 385-392
-
-
Sutcliffe, M.J.1
Hayes, F.R.F.2
Blundell, T.L.3
-
118
-
-
84855176719
-
Molecular dynamics simulation study explaining inhibitor selectivity in different class of histone deacetylases
-
Thangapandian S., John S., Lee K.W. Molecular dynamics simulation study explaining inhibitor selectivity in different class of histone deacetylases. Journal of Biomolecular Structure and Dynamics 2012, 29:677-698.
-
(2012)
Journal of Biomolecular Structure and Dynamics
, vol.29
, pp. 677-698
-
-
Thangapandian, S.1
John, S.2
Lee, K.W.3
-
119
-
-
58149144258
-
Ligand escape pathways and (Un)Binding free energy calculations for the hexameric insulin-phenol complex
-
Vashisth H., Abrams C.F. Ligand escape pathways and (Un)Binding free energy calculations for the hexameric insulin-phenol complex. Biophysical Journal 2008, 95:4193-4204.
-
(2008)
Biophysical Journal
, vol.95
, pp. 4193-4204
-
-
Vashisth, H.1
Abrams, C.F.2
-
120
-
-
84900496716
-
Homology modeling
-
Wiley-Blackwell, J. Gu, P.E. Bourne (Eds.)
-
Venselaar H., Krieger E., Vriend G. Homology modeling. Structural Bioinformatics 2011, 1035. Wiley-Blackwell. J. Gu, P.E. Bourne (Eds.).
-
(2011)
Structural Bioinformatics
, pp. 1035
-
-
Venselaar, H.1
Krieger, E.2
Vriend, G.3
-
121
-
-
22944467757
-
Computer "Experiments" on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules
-
Verlet L. Computer "Experiments" on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Physical Review 1967, 159:98-103.
-
(1967)
Physical Review
, vol.159
, pp. 98-103
-
-
Verlet, L.1
-
122
-
-
84869996349
-
Homology modeling a fast tool for drug discovery: current perspectives
-
Vyas V.K., Ukawala R.D., Ghate M., Chintha C. Homology modeling a fast tool for drug discovery: current perspectives. Indian Journal of Pharmacological Sciences 2012, 74:1-17.
-
(2012)
Indian Journal of Pharmacological Sciences
, vol.74
, pp. 1-17
-
-
Vyas, V.K.1
Ukawala, R.D.2
Ghate, M.3
Chintha, C.4
-
123
-
-
17744387920
-
All are not equal: a benchmark of different homology modeling programs
-
Wallner B., Elofsson A. All are not equal: a benchmark of different homology modeling programs. Protein Science 2005, 14:1315-1327.
-
(2005)
Protein Science
, vol.14
, pp. 1315-1327
-
-
Wallner, B.1
Elofsson, A.2
-
124
-
-
34250180904
-
Chromophore channeling in the G-protein coupled receptor rhodopsin
-
Wang T., Duan Y. Chromophore channeling in the G-protein coupled receptor rhodopsin. Journal of the American Chemical Society 2007, 129:6970-6971.
-
(2007)
Journal of the American Chemical Society
, vol.129
, pp. 6970-6971
-
-
Wang, T.1
Duan, Y.2
-
125
-
-
69749115865
-
Ligand entry and exit pathways in the [beta]2-Adrenergic receptor
-
Wang T., Duan Y. Ligand entry and exit pathways in the [beta]2-Adrenergic receptor. Journal of Molecular Biology 2009, 392:1102-1115.
-
(2009)
Journal of Molecular Biology
, vol.392
, pp. 1102-1115
-
-
Wang, T.1
Duan, Y.2
-
126
-
-
79952125246
-
Retinal release from opsin in molecular dynamics simulations
-
Wang T., Duan Y. Retinal release from opsin in molecular dynamics simulations. Journal of Molecular Recognition 2011, 24:350-358.
-
(2011)
Journal of Molecular Recognition
, vol.24
, pp. 350-358
-
-
Wang, T.1
Duan, Y.2
-
128
-
-
80051595050
-
Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza a virus M2
-
Wang J., Ma C., Fiorin G., Carnevale V., Wang T., Hu F., Lamb R.A., Pinto L.H., Hong M., Klein M.L., DeGrado W.F. Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza a virus M2. Journal of the American Chemical Society 2011, 133:12834-12841.
-
(2011)
Journal of the American Chemical Society
, vol.133
, pp. 12834-12841
-
-
Wang, J.1
Ma, C.2
Fiorin, G.3
Carnevale, V.4
Wang, T.5
Hu, F.6
Lamb, R.A.7
Pinto, L.H.8
Hong, M.9
Klein, M.L.10
DeGrado, W.F.11
-
129
-
-
33750467966
-
Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field
-
Weis A., Katebzadeh K., Söderhjelm P., Nilsson I., Ryde U. Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field. Journal of Medicinal Chemistry 2006, 49:6596-6606.
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, pp. 6596-6606
-
-
Weis, A.1
Katebzadeh, K.2
Söderhjelm, P.3
Nilsson, I.4
Ryde, U.5
-
130
-
-
34547566446
-
ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins
-
Wiederstein M., Sippl M. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research 2007, 35:W407-W410.
-
(2007)
Nucleic Acids Research
, vol.35
-
-
Wiederstein, M.1
Sippl, M.2
-
131
-
-
65249134982
-
Homology modelling: a review about the method on hand of the diabetic antigen GAD 65 structure prediction
-
Wiltgen M., Tilz G.P. Homology modelling: a review about the method on hand of the diabetic antigen GAD 65 structure prediction. Wiener Medizinische Wochenschrift 2009, 159:112-125.
-
(2009)
Wiener Medizinische Wochenschrift
, vol.159
, pp. 112-125
-
-
Wiltgen, M.1
Tilz, G.P.2
-
132
-
-
0033136019
-
Investigating a back door mechanism of actin phosphate release by steered molecular dynamics
-
Wriggers W., Schulten K. Investigating a back door mechanism of actin phosphate release by steered molecular dynamics. Proteins: Structure, Function, and Bioinformatics 1999, 35:262-273.
-
(1999)
Proteins: Structure, Function, and Bioinformatics
, vol.35
, pp. 262-273
-
-
Wriggers, W.1
Schulten, K.2
-
133
-
-
77949525702
-
Steered molecular dynamics simulations reveal the Likelier dissociation pathway of imatinib from its targeting kinases c-Kit and Abl
-
Yang L.-J., Zou J., Xie H.-Z., Li L.-L., Wei Y.-Q., Yang S.-Y. Steered molecular dynamics simulations reveal the Likelier dissociation pathway of imatinib from its targeting kinases c-Kit and Abl. PLoS One 2009, 4:e8470.
-
(2009)
PLoS One
, vol.4
-
-
Yang, L.-J.1
Zou, J.2
Xie, H.-Z.3
Li, L.-L.4
Wei, Y.-Q.5
Yang, S.-Y.6
-
135
-
-
39449115394
-
I-TASSER server for protein 3D structure prediction
-
Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 2008, 9:40.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 40
-
-
Zhang, Y.1
-
136
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
Šali A., Blundell T.L. Comparative protein modelling by satisfaction of spatial restraints. Journal of Molecular Biology 1993, 234:779-815.
-
(1993)
Journal of Molecular Biology
, vol.234
, pp. 779-815
-
-
Šali, A.1
Blundell, T.L.2
-
137
-
-
0000625523
-
Conjugate gradient minimization of the energy functional: a new method for electronic structure calculation
-
štich I., Car R., Parrinello M., Baroni S. Conjugate gradient minimization of the energy functional: a new method for electronic structure calculation. Physical Review B 1989, 39:4997-5004.
-
(1989)
Physical Review B
, vol.39
, pp. 4997-5004
-
-
štich, I.1
Car, R.2
Parrinello, M.3
Baroni, S.4
|