-
3
-
-
0039116206
-
Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: Results of a comprehensive survey
-
Szilágyi A, Závodszky P (2000) Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey. Structure 8: 493-504.
-
(2000)
Structure
, vol.8
, pp. 493-504
-
-
Szilágyi, A.1
Závodszky, P.2
-
4
-
-
0034017055
-
Factors enhancing protein thermostability
-
Kumar S, Tsai CJ, Nussinov R (2000) Factors enhancing protein thermostability. Protein Eng 13: 179-191. (Pubitemid 30237592)
-
(2000)
Protein Engineering
, vol.13
, Issue.3
, pp. 179-191
-
-
Kumar, S.1
Tsai, C.-J.2
Nussinov, R.3
-
5
-
-
36448932772
-
Molecular dynamics studies on the thermostability of family 11 xylanases
-
DOI 10.1093/protein/gzm056
-
Purmonen M, Valjakka J, Takkinen K, Laitinen T, Rouvinen J (2007) Molecular dynamics studies on the thermostability of family 11 xylanases. Protein Eng Des Sel 20: 551-559. (Pubitemid 350173525)
-
(2007)
Protein Engineering, Design and Selection
, vol.20
, Issue.11
, pp. 551-559
-
-
Purmonen, M.1
Valjakka, J.2
Takkinen, K.3
Laitinen, T.4
Rouvinen, J.5
-
6
-
-
5444250069
-
Correlation of local changes in the temperature-dependent conformational flexibility of thioredoxins with their thermostability
-
DOI 10.1023/B:RUBI.0000043784.51859.41
-
Polyansky AA, Kosinsky YA, Efremov RG (2004) Correlation of local changes in the temperature-dependent conformational flexibility of thioredoxins with their thermostability. Russ J Bioorganic Chem 30: 421-430. (Pubitemid 39360828)
-
(2004)
Russian Journal of Bioorganic Chemistry
, vol.30
, Issue.5
, pp. 421-430
-
-
Polyansky, A.A.1
Kosinsky, Y.A.2
Efremov, R.G.3
-
7
-
-
0031580199
-
Protein thermal stability, hydrogen bonds, and ion pairs
-
DOI 10.1006/jmbi.1997.1042
-
Vogt G, Woell S, Argos P (1997) Protein thermal stability, hydrogen bonds, and ion pairs. J Mol Biol 269: 631-643. (Pubitemid 27267875)
-
(1997)
Journal of Molecular Biology
, vol.269
, Issue.4
, pp. 631-643
-
-
Vogt, G.1
Woell, S.2
Argos, P.3
-
8
-
-
0011186093
-
Protein thermal stability: Hydrogen bonds or internal packing?
-
Vogt G, Argos P (1997) Protein thermal stability: hydrogen bonds or internal packing? Fold Des 2: S40-46. (Pubitemid 127740540)
-
(1997)
Folding and Design
, vol.2
, Issue.4
-
-
Vogt, G.1
Argos, P.2
-
9
-
-
0027367252
-
Structures of randomly generated mutants of T4 lysozyme show that protein stability can be enhanced by relaxation of strain and by improved hydrogen bonding via bound solvent
-
Pjura P, Matthews BW (1993) Structures of randomly generated mutants of T4 lysozyme show that protein stability can be enhanced by relaxation of strain and by improved hydrogen bonding via bound solvent. Protein Sci 2: 2226-2232. (Pubitemid 23354725)
-
(1993)
Protein Science
, vol.2
, Issue.12
, pp. 2226-2232
-
-
Pjura, P.1
Matthews, B.W.2
-
10
-
-
13244249836
-
The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures
-
DOI 10.1016/S0969-2126(01)00251-9
-
Yip KS, Stillman TJ, Britton KL, Artymiuk PJ, Baker PJ, et al. (1995) The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures. Structure 3: 1147-1158. (Pubitemid 3001432)
-
(1995)
Structure
, vol.3
, Issue.11
, pp. 1147-1158
-
-
Yip, K.S.1
Stillman, T.J.2
Britton, K.L.3
Artymiuk, P.J.4
Baker, P.J.5
Sedelnikova, S.E.6
Engel, P.C.7
Pasquo, A.8
Chiaraluce, R.9
Consalvi, V.10
Scandurra, R.11
Rice, D.W.12
-
11
-
-
79959612799
-
Stabilizing salt-bridge enhances protein thermostability by reducing the heat capacity change of unfolding
-
Chan CH, Yu TH, Wong KB (2011) Stabilizing salt-bridge enhances protein thermostability by reducing the heat capacity change of unfolding. PLoS One 6: e21624.
-
(2011)
PLoS One
, vol.6
-
-
Chan, C.H.1
Yu, T.H.2
Wong, K.B.3
-
12
-
-
0030741375
-
The crystal structure of citrate synthase from the hyperthermophilic archaeon Pyrococcus furiosus at 1.9 Å resolution
-
DOI 10.1021/bi9705321
-
Russell RJM, Ferguson JMC, Hough DW, Danson MJ, Taylor GL (1997) The Crystal Structure of Citrate Synthase from the Hyperthermophilic Archaeon Pyrococcus furiosus at 1.9 Å Resolution. Biochemistry 2960: 9983-9994. (Pubitemid 27357706)
-
(1997)
Biochemistry
, vol.36
, Issue.33
, pp. 9983-9994
-
-
Russell, R.J.M.1
Ferguson, J.M.C.2
Hough, D.W.3
Danson, M.J.4
Taylor, G.L.5
-
13
-
-
0024273441
-
Enhanced protein thermostability from designed mutations that interact with α-helix dipoles
-
DOI 10.1038/336651a0
-
Nicholson H, Becktel WJ, Matthews BW (1988) Enhanced protein thermostability from designed mutations that interact with α-helix dipoles. Nature 336: 651-656. (Pubitemid 19007945)
-
(1988)
Nature
, vol.336
, Issue.6200
, pp. 651-656
-
-
Nicholson, H.1
Becktel, W.J.2
Matthews, B.W.3
-
14
-
-
0024972502
-
Substantial increase of protein stability by multiple disulphide bonds
-
Matsumura M, Signor G, Matthews BW (1989) Substantial increase of protein stability by multiple disulphide bonds. Nature 342: 291-293.
-
(1989)
Nature
, vol.342
, pp. 291-293
-
-
Matsumura, M.1
Signor, G.2
Matthews, B.W.3
-
15
-
-
0028130117
-
Multiple proline substitutions cumulatively thermostabilize Bacillus cereus ATCC7064 oligo-1,6-glucosidase. Irrefragable proof supporting the proline rule
-
DOI 10.1111/j.1432-1033.1994.tb20051.x
-
Watanabe K, Masuda T, Ohashi H, Mihara H, Suzuki Y (1994) Multiple proline substitutions cumulatively thermostabilize Bacillus cereus ATCC7064 oligo-1,6-glucosidase. Eur J Biochem 283: 277-283. (Pubitemid 24379045)
-
(1994)
European Journal of Biochemistry
, vol.226
, Issue.2
, pp. 277-283
-
-
Watanabe, K.1
Masuda, T.2
Ohashi, H.3
Mihara, H.4
Suzuki, Y.5
-
16
-
-
0032516409
-
Protein thermostabilization by proline substitutions
-
DOI 10.1016/S1381-1177(97)00031-3, PII S1381117797000313
-
Watanabe K, Suzuki Y (1998) Protein thermostabilization by proline substitutions. J Mol Catal B Enzym 4: 167-180. (Pubitemid 28303932)
-
(1998)
Journal of Molecular Catalysis - B Enzymatic
, vol.4
, Issue.4
, pp. 167-180
-
-
Watanabe, K.1
Suzuki, Y.2
-
17
-
-
0030970741
-
Structural basis for thermostability and identification of potential active site residues for adenylate kinases from the archaeal genus Methanococcus
-
DOI 10.1002/(SICI)1097-0134(199705)28:1<117::AID-PR
-
Haney P, Konisky J, Koretke KK, Wolynes PG (1997) Structural basis for thermostability and identification of potential active site residues for adenylate kinases From the archaeal genus Methanococcus. Proteins Struct Funct Genet 130: 117-130. (Pubitemid 27194025)
-
(1997)
Proteins: Structure, Function and Genetics
, vol.28
, Issue.1
, pp. 117-130
-
-
Haney, P.1
Konisky, J.2
Koretke, K.K.3
Luthey-Schulten, Z.4
Wolynes, P.G.5
-
18
-
-
0029896617
-
An unusual route to thermostability disclosed by the comparison of Thermus thermophilus and Escherichia coli inorganic pyrophosphatases
-
Salminen T, Teplyakov A, Kankare J, Cooperman BS, Lahti R, et al. (1996) An unusual route to thermostability disclosed by the comparison of Thermus thermophilus and Escherichia coli inorganic pyrophosphatases. Protein Sci 5: 1014-1025. (Pubitemid 26172890)
-
(1996)
Protein Science
, vol.5
, Issue.6
, pp. 1014-1025
-
-
Salminen, T.1
Teplyakov, A.2
Kankare, J.3
Cooperman, B.S.4
Lahti, R.5
Goldman, A.6
-
19
-
-
84874797243
-
Hydrophobic environment is a key factor for the stability of thermophilic proteins
-
Gromiha MM, Pathak MC, Saraboji K, Ortlund EA, Gaucher EA (2013) Hydrophobic environment is a key factor for the stability of thermophilic proteins. Proteins Struct Funct Bioinforma 81: 715-721.
-
(2013)
Proteins Struct Funct Bioinforma
, vol.81
, pp. 715-721
-
-
Gromiha, M.M.1
Pathak, M.C.2
Saraboji, K.3
Ortlund, E.A.4
Gaucher, E.A.5
-
20
-
-
0035424955
-
Engineering proteins for thermostability: The use of sequence alignments versus rational design and directed evolution
-
DOI 10.1016/S0958-1669(00)00229-9
-
Lehmann M, Wyss M (2001) Engineering proteins for thermostability: the use of sequence alignments versus rational design and directed evolution. Curr Opin Biotechnol 12: 371-375. (Pubitemid 32718790)
-
(2001)
Current Opinion in Biotechnology
, vol.12
, Issue.4
, pp. 371-375
-
-
Lehmann, M.1
Wyss, M.2
-
21
-
-
0032919288
-
In vitro evolution of thermostable p53 variants
-
Matsumura I, Ellington AD (1999) In vitro evolution of thermostable p53 variants. Protein Sci 8: 731-740. (Pubitemid 29165403)
-
(1999)
Protein Science
, vol.8
, Issue.4
, pp. 731-740
-
-
Matsumura, I.1
Ellington, A.D.2
-
22
-
-
0032573217
-
Directed evolution of a thermostable esterase
-
DOI 10.1073/pnas.95.22.12809
-
Giver L, Gershenson A, Freskgard PO, Arnold FH (1998) Directed evolution of a thermostable esterase. Proc Natl Acad Sci U S A 95: 12809-12813. (Pubitemid 28509479)
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, Issue.22
, pp. 12809-12813
-
-
Giver, L.1
Gershenson, A.2
Freskgard, P.-O.3
Arnold, F.H.4
-
23
-
-
37849185207
-
Directed evolution of the thermostable xylanase from Thermomyces lanuginosus
-
DOI 10.1016/j.jbiotec.2006.06.015, PII S0168165606005323
-
Stephens DE, Rumbold K, Permaul K, Prior BA, Singh S (2007) Directed evolution of the thermostable xylanase from Thermomyces lanuginosus. J Biotechnol 127: 348-354. (Pubitemid 44827381)
-
(2007)
Journal of Biotechnology
, vol.127
, Issue.3
, pp. 348-354
-
-
Stephens, D.E.1
Rumbold, K.2
Permaul, K.3
Prior, B.A.4
Singh, S.5
-
24
-
-
0032973026
-
Directed evolution converts subtilisin E into a functional equivalent of thermitase
-
Zhao H, Arnold FH (1999) Directed evolution converts subtilisin E into a functional equivalent of thermitase. Protein Eng 12: 47-53. (Pubitemid 29050541)
-
(1999)
Protein Engineering
, vol.12
, Issue.1
, pp. 47-53
-
-
Zhao, H.1
Arnold, F.H.2
-
25
-
-
0040735677
-
Directed evolution of beta-glucosidase A from Paenibacillus polymyxa to thermal resistance
-
DOI 10.1074/jbc.275.18.13708
-
Gonzalez-Blasco G, Sanz-Aparicio J, Gonzalez B, Hermoso JA, Polaina J (2000) Directed evolution of beta-glucosidase A from Paenibacillus polymyxa to thermal resistance. J Biol Chem 275: 13708-13712. (Pubitemid 30257441)
-
(2000)
Journal of Biological Chemistry
, vol.275
, Issue.18
, pp. 13708-13712
-
-
Gonzalez-Blasco, G.1
Sanz-Aparicio, J.2
Gonzalez, B.3
Hermoso, J.A.4
Polaina, J.5
-
26
-
-
4143110558
-
Structural basis of selection and thermostability of laboratory evolved Bacillus subtilis lipase
-
DOI 10.1016/j.jmb.2004.06.059, PII S0022283604007636
-
Acharya P, Rajakumara E, Sankaranarayanan R, Rao NM (2004) Structural basis of selection and thermostability of laboratory evolved Bacillus subtilis lipase. J Mol Biol 341: 1271-1281. (Pubitemid 39092314)
-
(2004)
Journal of Molecular Biology
, vol.341
, Issue.5
, pp. 1271-1281
-
-
Acharya, P.1
Rajakumara, E.2
Sankaranarayanan, R.3
Rao, N.M.4
-
27
-
-
47049084664
-
Thermostable Bacillus subtilis lipases: In vitro evolution and structural insight
-
Ahmad S, Kamal MZ, Sankaranarayanan R, Rao NM (2008) Thermostable Bacillus subtilis lipases: in vitro evolution and structural insight. J Mol Biol 381: 324-340.
-
(2008)
J Mol Biol
, vol.381
, pp. 324-340
-
-
Ahmad, S.1
Kamal, M.Z.2
Sankaranarayanan, R.3
Rao, N.M.4
-
28
-
-
80054692390
-
In vitro evolved non-aggregating and thermostable lipase: Structural and thermodynamic investigation
-
Kamal MZ, Ahmad S, Molugu TR, Vijayalakshmi A, Deshmukh MV, et al. (2011) In vitro evolved non-aggregating and thermostable lipase: structural and thermodynamic investigation. J Mol Biol 413: 726-741.
-
(2011)
J Mol Biol
, vol.413
, pp. 726-741
-
-
Kamal, M.Z.1
Ahmad, S.2
Molugu, T.R.3
Vijayalakshmi, A.4
Deshmukh, M.V.5
-
29
-
-
41149104308
-
Allostery: Absence of a change in shape does not imply that allostery is not at play
-
Tsai C, Del Sol A, Nussinov R (2009) Allostery: Absence of a change in shape does not imply that allostery is not at play. J Mol Biol 378: 1-11.
-
(2009)
J Mol Biol
, vol.378
, pp. 1-11
-
-
Tsai, C.1
Del Sol, A.2
Nussinov, R.3
-
30
-
-
9944223645
-
Network properties of protein structures
-
Bagler G, Sinha S (2008) Network properties of protein structures. Phys A Stat Mech its Appl 346: 27-33.
-
(2008)
Phys A Stat Mech Its Appl
, vol.346
, pp. 27-33
-
-
Bagler, G.1
Sinha, S.2
-
31
-
-
33745461893
-
Residues crucial for maintaining short paths in network communication mediate signaling in proteins
-
Del Sol A, Fujihashi H, Amoros D, Nussinov R (2006) Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Mol Syst Biol 2: 2006.0019.
-
(2006)
Mol Syst Biol
, vol.2
-
-
Del Sol, A.1
Fujihashi, H.2
Amoros, D.3
Nussinov, R.4
-
32
-
-
72949085966
-
Ligand dependent intra and inter subunit communication in human tryptophanyl tRNA synthetase as deduced from the dynamics of structure networks
-
Hansia P, Ghosh A, Vishveshwara S (2009) Ligand dependent intra and inter subunit communication in human tryptophanyl tRNA synthetase as deduced from the dynamics of structure networks. Mol Biosyst 5: 1860-1872.
-
(2009)
Mol Biosyst
, vol.5
, pp. 1860-1872
-
-
Hansia, P.1
Ghosh, A.2
Vishveshwara, S.3
-
33
-
-
34547909602
-
Assortative mixing in protein contact networks and protein folding kinetics
-
DOI 10.1093/bioinformatics/btm257
-
Bagler G, Sinha S (2007) Assortative mixing in Protein Contact Networks and protein folding kinetics. Bioinformatics 23: 1760-1767. (Pubitemid 47250308)
-
(2007)
Bioinformatics
, vol.23
, Issue.14
, pp. 1760-1767
-
-
Bagler, G.1
Sinha, S.2
-
34
-
-
0035946913
-
The crystal structure of Bacillus subtilis lipase: A minimal α/beta hydrolase fold enzyme
-
DOI 10.1006/jmbi.2001.4659
-
Pouderoyen G, Eggert T, Jaeger K-E, Dijkstra BW (2001) The crystal structure of Bacillus subtilis lipase: a minimal a/b hydrolase fold enzyme. J Mol Biol 309: 215-226. (Pubitemid 32553519)
-
(2001)
Journal of Molecular Biology
, vol.309
, Issue.1
, pp. 215-226
-
-
Van Pouderoyen, G.1
Eggert, T.2
Jaeger, K.-E.3
Dijkstra, B.W.4
-
35
-
-
0032482432
-
Collective dynamics of "small-world" networks
-
Watts DJ, Strogatz SH (1998) Collective dynamics of "small- world" networks. Nature 393: 440-442.
-
(1998)
Nature
, vol.393
, pp. 440-442
-
-
Watts, D.J.1
Strogatz, S.H.2
-
36
-
-
84859722834
-
Role of active site rigidity in activity: MD simulation and fluorescence study on a lipase mutant
-
Kamal MZ, Mohammad TAS, Krishnamoorthy G, Rao NM (2012) Role of active site rigidity in activity: MD simulation and fluorescence study on a lipase mutant. PLoS One 7: e35188.
-
(2012)
PLoS One
, vol.7
-
-
Kamal, M.Z.1
Mohammad, T.A.S.2
Krishnamoorthy, G.3
Rao, N.M.4
-
37
-
-
34548815693
-
Modular architecture of protein structures and allosteric communications: Potential implications for signaling proteins and regulatory linkages
-
Del Sol A, Araúzo-Bravo MJ, Amoros D, Nussinov R (2007) Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages. Genome Biol 8: R92.
-
(2007)
Genome Biol
, vol.8
-
-
Del Sol, A.1
Araúzo-Bravo, M.J.2
Amoros, D.3
Nussinov, R.4
-
38
-
-
0032742598
-
Helix-stabilizing factors and stabilization of thermophilic proteins: An X-ray based study
-
Facchiano A, Colonna G, Ragone R (1999) Helix-stabilizing factors and stabilization of thermophilic proteins: an X-ray based study. Protein Eng 12: 893.
-
(1999)
Protein Eng
, vol.12
, pp. 893
-
-
Facchiano, A.1
Colonna, G.2
Ragone, R.3
-
39
-
-
0036902235
-
Close-range electrostatic interactions in proteins
-
DOI 10.1002/1439-7633(20020703)3:7<604::AID-CBIC604
-
Kumar S, Nussinov R (2002) Close range electrostatic interactions in proteins. ChemBioChem 3: 604-617. (Pubitemid 36004524)
-
(2002)
ChemBioChem
, vol.3
, Issue.7
, pp. 604-617
-
-
Kumar, S.1
Nussinov, R.2
-
40
-
-
0032561237
-
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
-
80
-
Duan Y, Kollman PA (1998) Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science (80-) 282: 740-744.
-
(1998)
Science
, vol.282
, pp. 740-744
-
-
Duan, Y.1
Kollman, P.A.2
-
41
-
-
0036968512
-
Increasing temperature accelerates protein unfolding without changing the pathway of unfolding
-
DOI 10.1016/S0022-2836(02)00672-1
-
Day R, Bennion BJ, Ham S, Daggett V (2002) Increasing temperature accelerates protein unfolding without changing the pathway of unfolding. J Mol Biol 322: 189-203. (Pubitemid 36132678)
-
(2002)
Journal of Molecular Biology
, vol.322
, Issue.1
, pp. 189-203
-
-
Day, R.1
Bennion, B.J.2
Ham, S.3
Daggett, V.4
-
42
-
-
84875170915
-
Protein Contact Networks: An Emerging Paradigm in Chemistry
-
Paola L Di, Ruvo M De PP, Santoni D, Giuliani A (2013) Protein Contact Networks: An Emerging Paradigm in Chemistry. Chem Rev 113: 1598-1613.
-
(2013)
Chem Rev
, vol.113
, pp. 1598-1613
-
-
Di Paola, L.1
De Ruvo, M.2
P, P.3
Santoni, D.4
Giuliani, A.5
-
43
-
-
84866463338
-
Versatility from protein disorder
-
802
-
Babu MM, Kriwacki RW, Pappu RV (2012) Versatility from protein disorder. Science (802) 337: 1460-1461.
-
(2012)
Science
, vol.337
, pp. 1460-1461
-
-
Babu, M.M.1
Kriwacki, R.W.2
Pappu, R.V.3
-
44
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucleic Acid Res 28: 235-242. (Pubitemid 30047768)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
45
-
-
33646202578
-
Multiple alignment of protein structure in three dimensions
-
Krissinel E, Henrick K (2005) Multiple alignment of protein structure in three dimensions. Lect Notes Comput Sci 3695: 67-68.
-
(2005)
Lect Notes Comput Sci
, vol.3695
, pp. 67-68
-
-
Krissinel, E.1
Henrick, K.2
-
47
-
-
1842464687
-
Inter-residue interactions in protein folding and stability
-
DOI 10.1016/j.pbiomolbio.2003.09.003, PII S0079610703000816
-
Gromiha MM, Selvaraj S (2004) Inter-residue interactions in protein folding and stability. Prog Biophys Mol Biol 86: 235-277. (Pubitemid 39027234)
-
(2004)
Progress in Biophysics and Molecular Biology
, vol.86
, Issue.2
, pp. 235-277
-
-
Gromiha, M.M.1
Selvaraj, S.2
-
48
-
-
43349094507
-
The igraph software package for complex network research
-
Csardi G, Nepusz T (2006) The igraph software package for complex network research. Interjournal Complex Syst: 1695.
-
(2006)
Interjournal Complex Syst
, vol.1695
-
-
Csardi, G.1
Nepusz, T.2
-
49
-
-
84859865809
-
R: A Language and Environment for Statistical Computing
-
Development Core Team R Available
-
Development Core Team R (2010) R: A Language and Environment for Statistical Computing. R Found Stat Comput 1: 409. Available: http://www.rproject.org.
-
(2010)
R Found Stat Comput
, vol.1
, pp. 409
-
-
-
50
-
-
41349117788
-
Finding community structure in very large networks
-
Clauset A, Newman MEJ, Moore C (2004) Finding community structure in very large networks. Phys Rev E 70: 066111.
-
(2004)
Phys Rev E
, vol.70
, pp. 066111
-
-
Clauset, A.1
Newman, M.E.J.2
Moore, C.3
-
51
-
-
84875592758
-
GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit
-
Pronk S, Pall S, Schulz R, Larsson P, Bjelkmar P, et al. (2013) GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29: 845-854.
-
(2013)
Bioinformatics
, vol.29
, pp. 845-854
-
-
Pronk, S.1
Pall, S.2
Schulz, R.3
Larsson, P.4
Bjelkmar, P.5
-
52
-
-
59649095963
-
A short guide for molecular dynamics simulations of RNA systems
-
Hashem Y, Auffinger P (2009) A short guide for molecular dynamics simulations of RNA systems. Methods 47: 187-197.
-
(2009)
Methods
, vol.47
, pp. 187-197
-
-
Hashem, Y.1
Auffinger, P.2
-
53
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, et al. (1995) A smooth particle mesh Ewald method. J Chem Phys 103: 31-34.
-
(1995)
J Chem Phys
, vol.103
, pp. 31-34
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
-
54
-
-
0000388705
-
LINCS: A Linear Constraint Solver for molecular simulations
-
Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) LINCS: A linear constraint solver for molecular simulations. J Comput Chem 18: 1463-1472. (Pubitemid 127637344)
-
(1997)
Journal of Computational Chemistry
, vol.18
, Issue.12
, pp. 1463-1472
-
-
Hess, B.1
Bekker, H.2
Berendsen, H.J.C.3
Fraaije, J.G.E.M.4
-
55
-
-
33846086933
-
Canonical sampling through velocity rescaling
-
Bussi G, Donadio D, Parrinello M (2007) Canonical sampling through velocity rescaling. J Chem Phys 126: 014101.
-
(2007)
J Chem Phys
, vol.126
, pp. 014101
-
-
Bussi, G.1
Donadio, D.2
Parrinello, M.3
-
56
-
-
0019707626
-
Polymorphic transitions in single crystals: A new molecular dynamics method
-
Parrinello M, Rahman A (1981) Polymorphic transitions in single crystals: A new molecular dynamics method. J Appl Phys 52: 7182.
-
(1981)
J Appl Phys
, vol.52
, pp. 7182
-
-
Parrinello, M.1
Rahman, A.2
-
57
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
59
-
-
0029878720
-
VMD-Visual Molecular Dynamics
-
Available
-
Humphrey W, Dalke A, Schulten K (1996) VMD-Visual Molecular Dynamics. J Mol Graph 14: 33-38. Available: http://www.ks.uiuc.edu/Research/vmd/.
-
(1996)
J Mol Graph
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
60
-
-
0042121261
-
POPS: A fast algorithm for solvent accessible surface areas at atomic and residue level
-
DOI 10.1093/nar/gkg601
-
Cavallo L, Kleinjung J, Fraternali F, Allende S, Unit B (2003) POPS: a fast algorithm for solvent accessible surface areas at atomic and residue level. Nucleic Acid Res 31: 3364-3366. (Pubitemid 37442160)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.13
, pp. 3364-3366
-
-
Cavallo, L.1
Kleinjung, J.2
Fraternali, F.3
|