-
1
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28: 235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
-
2
-
-
0004702255
-
Model of Protein Folding - Inclusion of Short-Range, Medium-Range, and Long-Range Interactions
-
Tanaka S, Scheraga HA, (1975) Model of Protein Folding- Inclusion of Short-Range, Medium-Range, and Long-Range Interactions. Proceedings of the National Academy of Sciences of the United States of America 72: 3802-3806.
-
(1975)
Proceedings of the National Academy of Sciences of the United States of America
, vol.72
, pp. 3802-3806
-
-
Tanaka, S.1
Scheraga, H.A.2
-
3
-
-
33845377127
-
Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation
-
Miyazawa S, Jernigan RL, (1985) Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 18: 534-552.
-
(1985)
Macromolecules
, vol.18
, pp. 534-552
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
4
-
-
0029919190
-
Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
-
Miyazawa S, Jernigan RL, (1996) Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 256: 623-644.
-
(1996)
J Mol Biol
, vol.256
, pp. 623-644
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
8
-
-
84990469589
-
Cooperative ligand binding on multidimensional lattices: Bethe approximation
-
Miyazawa S, (1983) Cooperative ligand binding on multidimensional lattices: Bethe approximation. Biopolymers 22: 2253-2271.
-
(1983)
Biopolymers
, vol.22
, pp. 2253-2271
-
-
Miyazawa, S.1
-
14
-
-
0025341310
-
Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
-
Sippl MJ, (1990) Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 213: 859-883.
-
(1990)
J Mol Biol
, vol.213
, pp. 859-883
-
-
Sippl, M.J.1
-
15
-
-
0035882533
-
A distance-dependent atomic knowledge-based potential for improved protein structure selection
-
Lu H, Skolnick J, (2001) A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins-Structure Function and Genetics 44: 223-232.
-
(2001)
Proteins-Structure Function and Genetics
, vol.44
, pp. 223-232
-
-
Lu, H.1
Skolnick, J.2
-
16
-
-
0032488962
-
An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
-
Samudrala R, Moult J, (1998) An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. Journal of Molecular Biology 275: 895-916.
-
(1998)
Journal of Molecular Biology
, vol.275
, pp. 895-916
-
-
Samudrala, R.1
Moult, J.2
-
17
-
-
1942423584
-
Continuous anisotropic representation of coarse-grained potentials for proteins by spherical harmonics synthesis
-
Buchete NV, Straub JE, Thirumalai D, (2004) Continuous anisotropic representation of coarse-grained potentials for proteins by spherical harmonics synthesis. Journal of Molecular Graphics & Modelling 22: 441-450.
-
(2004)
Journal of Molecular Graphics & Modelling
, vol.22
, pp. 441-450
-
-
Buchete, N.V.1
Straub, J.E.2
Thirumalai, D.3
-
18
-
-
22944468214
-
How effective for fold recognition is a potential of mean force that includes relative orientations between contacting residues in proteins?
-
Miyazawa S, Jernigan RL, (2005) How effective for fold recognition is a potential of mean force that includes relative orientations between contacting residues in proteins? J Chem Phys 122: 024901.
-
(2005)
J Chem Phys
, vol.122
, pp. 024901
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
19
-
-
39349092548
-
Tri-residue contact potential: a new knowledge-based energetic method
-
Lin W, Sun F, Rao ZH, (2002) Tri-residue contact potential: a new knowledge-based energetic method. Progress in Natural Science 12: 826-840.
-
(2002)
Progress in Natural Science
, vol.12
, pp. 826-840
-
-
Lin, W.1
Sun, F.2
Rao, Z.H.3
-
20
-
-
0026726481
-
Topology fingerprint approach to the inverse protein folding problem
-
Godzik A, Kolinski A, Skolnick J, (1992) Topology fingerprint approach to the inverse protein folding problem. J Mol Biol 227: 227-238.
-
(1992)
J Mol Biol
, vol.227
, pp. 227-238
-
-
Godzik, A.1
Kolinski, A.2
Skolnick, J.3
-
21
-
-
0027050011
-
Sequence-structure matching in globular proteins: application to supersecondary and tertiary structure determination
-
Godzik A, Skolnick J, (1992) Sequence-structure matching in globular proteins: application to supersecondary and tertiary structure determination. Proc Natl Acad Sci U S A 89: 12098-12102.
-
(1992)
Proc Natl Acad Sci U S A
, vol.89
, pp. 12098-12102
-
-
Godzik, A.1
Skolnick, J.2
-
22
-
-
0030054951
-
Delaunay tessellation of proteins: four body nearest-neighbor propensities of amino acid residues
-
Singh RK, Tropsha A, Vaisman II, (1996) Delaunay tessellation of proteins: four body nearest-neighbor propensities of amino acid residues. J Comput Biol 3: 213-221.
-
(1996)
J Comput Biol
, vol.3
, pp. 213-221
-
-
Singh, R.K.1
Tropsha, A.2
Vaisman, I.I.3
-
23
-
-
0030632384
-
Multi-body interactions within the graph of protein structure
-
Munson PJ, Singh RK, (1997) Multi-body interactions within the graph of protein structure. Proc Int Conf Intell Syst Mol Biol 5: 198-201.
-
(1997)
Proc Int Conf Intell Syst Mol Biol
, vol.5
, pp. 198-201
-
-
Munson, P.J.1
Singh, R.K.2
-
24
-
-
0030806961
-
Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment
-
Munson PJ, Singh RK, (1997) Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment. Protein Sci 6: 1467-1481.
-
(1997)
Protein Sci
, vol.6
, pp. 1467-1481
-
-
Munson, P.J.1
Singh, R.K.2
-
25
-
-
16344396587
-
A multibody, whole-residue potential for protein structures, with testing by Monte Carlo simulated annealing
-
Mayewski S, (2005) A multibody, whole-residue potential for protein structures, with testing by Monte Carlo simulated annealing. Proteins 59: 152-169.
-
(2005)
Proteins
, vol.59
, pp. 152-169
-
-
Mayewski, S.1
-
26
-
-
0035943455
-
Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations
-
Carter CW Jr, LeFebvre BC, Cammer SA, Tropsha A, Edgell MH, (2001) Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations. Journal of Molecular Biology 311: 625-638.
-
(2001)
Journal of Molecular Biology
, vol.311
, pp. 625-638
-
-
Carter Jr., C.W.1
LeFebvre, B.C.2
Cammer, S.A.3
Tropsha, A.4
Edgell, M.H.5
-
28
-
-
36448967447
-
Four-Body Scoring Function for Mutagenesis
-
Deutsch C, Krishnamoorthy B, (2007) Four-Body Scoring Function for Mutagenesis. Bioinformatics 23: 3009-3015.
-
(2007)
Bioinformatics
, vol.23
, pp. 3009-3015
-
-
Deutsch, C.1
Krishnamoorthy, B.2
-
29
-
-
34249938371
-
Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys
-
Feng YP, Kloczkowski A, Jernigan RL, (2007) Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys. Proteins-Structure Function and Bioinformatics 68: 57-66.
-
(2007)
Proteins-Structure Function and Bioinformatics
, vol.68
, pp. 57-66
-
-
Feng, Y.P.1
Kloczkowski, A.2
Jernigan, R.L.3
-
30
-
-
0042889108
-
Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations
-
Krishnamoorthy B, Tropsha A, (2003) Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations. Bioinformatics 19: 1540-1548.
-
(2003)
Bioinformatics
, vol.19
, pp. 1540-1548
-
-
Krishnamoorthy, B.1
Tropsha, A.2
-
32
-
-
0027490731
-
Recognition of errors in three-dimensional structures of proteins
-
Sippl MJ, (1993) Recognition of errors in three-dimensional structures of proteins. Proteins 17: 355-362.
-
(1993)
Proteins
, vol.17
, pp. 355-362
-
-
Sippl, M.J.1
-
33
-
-
0029844461
-
Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of protein structures: atomic burial position and pairwise non-bonded interactions
-
DeBolt SE, Skolnick J, (1996) Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of protein structures: atomic burial position and pairwise non-bonded interactions. Protein Eng 9: 637-655.
-
(1996)
Protein Eng
, vol.9
, pp. 637-655
-
-
DeBolt, S.E.1
Skolnick, J.2
-
34
-
-
0034560338
-
Discrimination of near-native protein structures from misfolded models by empirical free energy functions
-
Gatchell DW, Dennis S, Vajda S, (2000) Discrimination of near-native protein structures from misfolded models by empirical free energy functions. Proteins 41: 518-534.
-
(2000)
Proteins
, vol.41
, pp. 518-534
-
-
Gatchell, D.W.1
Dennis, S.2
Vajda, S.3
-
35
-
-
25844459522
-
Combining electron microscopy and comparative protein structure modeling
-
Topf M, Sali A, (2005) Combining electron microscopy and comparative protein structure modeling. Curr Opin Struct Biol 15: 578-585.
-
(2005)
Curr Opin Struct Biol
, vol.15
, pp. 578-585
-
-
Topf, M.1
Sali, A.2
-
36
-
-
33645075435
-
Refinement of protein structures by iterative comparative modeling and CryoEM density fitting
-
Topf M, Baker ML, Marti-Renom MA, Chiu W, Sali A, (2006) Refinement of protein structures by iterative comparative modeling and CryoEM density fitting. J Mol Biol 357: 1655-1668.
-
(2006)
J Mol Biol
, vol.357
, pp. 1655-1668
-
-
Topf, M.1
Baker, M.L.2
Marti-Renom, M.A.3
Chiu, W.4
Sali, A.5
-
37
-
-
0026785519
-
Contact potential that recognizes the correct folding of globular proteins
-
Maiorov VN, Crippen GM, (1992) Contact potential that recognizes the correct folding of globular proteins. J Mol Biol 227: 876-888.
-
(1992)
J Mol Biol
, vol.227
, pp. 876-888
-
-
Maiorov, V.N.1
Crippen, G.M.2
-
38
-
-
0026704815
-
Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations
-
Sippl MJ, Weitckus S, (1992) Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations. Proteins 13: 258-271.
-
(1992)
Proteins
, vol.13
, pp. 258-271
-
-
Sippl, M.J.1
Weitckus, S.2
-
39
-
-
0027318317
-
An empirical energy function for threading protein sequence through the folding motif
-
Bryant SH, Lawrence CE, (1993) An empirical energy function for threading protein sequence through the folding motif. Proteins 16: 92-112.
-
(1993)
Proteins
, vol.16
, pp. 92-112
-
-
Bryant, S.H.1
Lawrence, C.E.2
-
41
-
-
0033566614
-
An empirical energy potential with a reference state for protein fold and sequence recognition
-
Miyazawa S, Jernigan RL, (1999) An empirical energy potential with a reference state for protein fold and sequence recognition. Proteins 36: 357-369.
-
(1999)
Proteins
, vol.36
, pp. 357-369
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
42
-
-
0033867374
-
Identifying sequence-structure pairs undetected by sequence alignments
-
Miyazawa S, Jernigan RL, (2000) Identifying sequence-structure pairs undetected by sequence alignments. Protein Eng 13: 459-475.
-
(2000)
Protein Eng
, vol.13
, pp. 459-475
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
43
-
-
0033970623
-
Derivation of protein-specific pair potentials based on weak sequence fragment similarity
-
Skolnick J, Kolinski A, Ortiz A, (2000) Derivation of protein-specific pair potentials based on weak sequence fragment similarity. Proteins 38: 3-16.
-
(2000)
Proteins
, vol.38
, pp. 3-16
-
-
Skolnick, J.1
Kolinski, A.2
Ortiz, A.3
-
44
-
-
0025008445
-
Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force
-
Hendlich M, Lackner P, Weitckus S, Floeckner H, Froschauer R, et al. (1990) Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force. J Mol Biol 216: 167-180.
-
(1990)
J Mol Biol
, vol.216
, pp. 167-180
-
-
Hendlich, M.1
Lackner, P.2
Weitckus, S.3
Floeckner, H.4
Froschauer, R.5
-
45
-
-
0026539511
-
Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds
-
Casari G, Sippl MJ, (1992) Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds. J Mol Biol 224: 725-732.
-
(1992)
J Mol Biol
, vol.224
, pp. 725-732
-
-
Casari, G.1
Sippl, M.J.2
-
46
-
-
0028351287
-
An improved pair potential to recognize native protein folds
-
Bauer A, Beyer A, (1994) An improved pair potential to recognize native protein folds. Proteins 18: 254-261.
-
(1994)
Proteins
, vol.18
, pp. 254-261
-
-
Bauer, A.1
Beyer, A.2
-
47
-
-
0032488962
-
An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
-
Samudrala R, Moult J, (1998) An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 275: 895-916.
-
(1998)
J Mol Biol
, vol.275
, pp. 895-916
-
-
Samudrala, R.1
Moult, J.2
-
48
-
-
0032929780
-
Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
-
Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C, et al. (1999) Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 34: 82-95.
-
(1999)
Proteins
, vol.34
, pp. 82-95
-
-
Simons, K.T.1
Ruczinski, I.2
Kooperberg, C.3
Fox, B.A.4
Bystroff, C.5
-
49
-
-
70349337592
-
Native secondary structure topology has near minimum contact energy among all possible geometrically constrained topologies
-
Sun WT, He J, (2009) Native secondary structure topology has near minimum contact energy among all possible geometrically constrained topologies. Proteins-Structure Function and Bioinformatics 77: 159-173.
-
(2009)
Proteins-Structure Function and Bioinformatics
, vol.77
, pp. 159-173
-
-
Sun, W.T.1
He, J.2
-
50
-
-
60849119541
-
Reduction of the secondary structure topological space through direct estimation of the contact energy formed by the secondary structures
-
Sun WT, He J, (2009) Reduction of the secondary structure topological space through direct estimation of the contact energy formed by the secondary structures. BMC Bioinformatics 10 (suppl 1): S40.
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.SUPPL. 1
-
-
Sun, W.T.1
He, J.2
-
51
-
-
75149136663
-
Structure prediction for the helical skeletons detected from the low resolution protein density map
-
Al Nasr K, Sun WT, He J, (2010) Structure prediction for the helical skeletons detected from the low resolution protein density map. BMC Bioinformatics 11 (suppl 1): S44.
-
(2010)
BMC Bioinformatics
, vol.11
, Issue.SUPPL. 1
-
-
Al Nasr, K.1
Sun, W.T.2
He, J.3
-
52
-
-
0025830469
-
A method to identify protein sequences that fold into a known three-dimensional structure
-
Bowie JU, Luthy R, Eisenberg D, (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science 253: 164-170.
-
(1991)
Science
, vol.253
, pp. 164-170
-
-
Bowie, J.U.1
Luthy, R.2
Eisenberg, D.3
-
53
-
-
0027503403
-
Reduced representation model of protein structure prediction: statistical potential and genetic algorithms
-
Sun S, (1993) Reduced representation model of protein structure prediction: statistical potential and genetic algorithms. Protein Sci 2: 762-785.
-
(1993)
Protein Sci
, vol.2
, pp. 762-785
-
-
Sun, S.1
-
54
-
-
0034308163
-
Distance-dependent, pair potential for protein folding: results from linear optimization
-
Tobi D, Elber R, (2000) Distance-dependent, pair potential for protein folding: results from linear optimization. Proteins 41: 40-46.
-
(2000)
Proteins
, vol.41
, pp. 40-46
-
-
Tobi, D.1
Elber, R.2
-
55
-
-
0034237798
-
On the design and analysis of protein folding potentials
-
Tobi D, Shafran G, Linial N, Elber R, (2000) On the design and analysis of protein folding potentials. Proteins 40: 71-85.
-
(2000)
Proteins
, vol.40
, pp. 71-85
-
-
Tobi, D.1
Shafran, G.2
Linial, N.3
Elber, R.4
-
56
-
-
44349106520
-
Identifying folding nucleus based on residue contact networks of proteins
-
Li J, Wang J, Wang W, (2008) Identifying folding nucleus based on residue contact networks of proteins. Proteins 71: 1899-1907.
-
(2008)
Proteins
, vol.71
, pp. 1899-1907
-
-
Li, J.1
Wang, J.2
Wang, W.3
-
57
-
-
0033578690
-
Identification of side-chain clusters in protein structures by a graph spectral method
-
Kannan N, Vishveshwara S, (1999) Identification of side-chain clusters in protein structures by a graph spectral method. J Mol Biol 292: 441-464.
-
(1999)
J Mol Biol
, vol.292
, pp. 441-464
-
-
Kannan, N.1
Vishveshwara, S.2
-
58
-
-
0242720597
-
Uncovering network systems within protein structures
-
Greene LH, Higman VA, (2003) Uncovering network systems within protein structures. J Mol Biol 334: 781-791.
-
(2003)
J Mol Biol
, vol.334
, pp. 781-791
-
-
Greene, L.H.1
Higman, V.A.2
-
59
-
-
70049115535
-
Four Distances between Pairs of Amino Acids Provide a Precise Description of their Interaction
-
Cohen M, Potapov V, Schreiber G, (2009) Four Distances between Pairs of Amino Acids Provide a Precise Description of their Interaction. Plos Computational Biology 5: e1000470.
-
(2009)
Plos Computational Biology
, vol.5
-
-
Cohen, M.1
Potapov, V.2
Schreiber, G.3
-
60
-
-
0036145846
-
Statistical potentials for fold assessment
-
Melo F, Sanchez R, Sali A, (2002) Statistical potentials for fold assessment. Protein Sci 11: 430-448.
-
(2002)
Protein Sci
, vol.11
, pp. 430-448
-
-
Melo, F.1
Sanchez, R.2
Sali, A.3
-
61
-
-
0036838311
-
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
-
Zhou H, Zhou Y, (2002) Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 11: 2714-2726.
-
(2002)
Protein Sci
, vol.11
, pp. 2714-2726
-
-
Zhou, H.1
Zhou, Y.2
-
62
-
-
0016610491
-
Computer simulation of protein folding
-
Levitt M, Warshel A, (1975) Computer simulation of protein folding. Nature 253: 694-698.
-
(1975)
Nature
, vol.253
, pp. 694-698
-
-
Levitt, M.1
Warshel, A.2
-
63
-
-
0017157584
-
A simplified representation of protein conformations for rapid simulation of protein folding
-
Levitt M, (1976) A simplified representation of protein conformations for rapid simulation of protein folding. J Mol Biol 104: 59-107.
-
(1976)
J Mol Biol
, vol.104
, pp. 59-107
-
-
Levitt, M.1
-
64
-
-
0033514939
-
Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K
-
Lee J, Liwo A, Scheraga HA, (1999) Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K. Proc Natl Acad Sci U S A 96: 2025-2030.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 2025-2030
-
-
Lee, J.1
Liwo, A.2
Scheraga, H.A.3
-
65
-
-
0035797727
-
Optimization of parameters in macromolecular potential energy functions by conformational space annealing
-
Lee J, Ripoll DR, Czaplewski C, Pillardy J, Wedemeyer WJ, et al. (2001) Optimization of parameters in macromolecular potential energy functions by conformational space annealing. Journal of Physical Chemistry B 105: 7291-7298.
-
(2001)
Journal of Physical Chemistry B
, vol.105
, pp. 7291-7298
-
-
Lee, J.1
Ripoll, D.R.2
Czaplewski, C.3
Pillardy, J.4
Wedemeyer, W.J.5
-
66
-
-
0037133165
-
A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: Application to the UNRES force field
-
Liwo A, Arlukowicz P, Czaplewski C, Oldziej S, Pillardy J, et al. (2002) A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: Application to the UNRES force field. Proceedings of the National Academy of Sciences of the United States of America 99: 1937-1942.
-
(2002)
Proceedings of the National Academy of Sciences of the United States of America
, vol.99
, pp. 1937-1942
-
-
Liwo, A.1
Arlukowicz, P.2
Czaplewski, C.3
Oldziej, S.4
Pillardy, J.5
-
67
-
-
0017588168
-
Study of Preferred Environment of Amino-Acid Residues in Globular Proteins
-
Manavalan P, Ponnuswamy PK, (1977) Study of Preferred Environment of Amino-Acid Residues in Globular Proteins. Archives of Biochemistry and Biophysics 184: 476-487.
-
(1977)
Archives of Biochemistry and Biophysics
, vol.184
, pp. 476-487
-
-
Manavalan, P.1
Ponnuswamy, P.K.2
-
68
-
-
0018077908
-
Hydrophobic Character of Amino-Acid Residues in Globular Proteins
-
Manavalan P, Ponnuswamy PK, (1978) Hydrophobic Character of Amino-Acid Residues in Globular Proteins. Nature 275: 673-674.
-
(1978)
Nature
, vol.275
, pp. 673-674
-
-
Manavalan, P.1
Ponnuswamy, P.K.2
-
69
-
-
0033382389
-
Amino acid clustering pattern and medium and long-range interactions in (alpha/beta)(8) barrel proteins
-
Gromiha MM, Selvaraj S, (1999) Amino acid clustering pattern and medium and long-range interactions in (alpha/beta)(8) barrel proteins. Periodicum Biologorum 101: 333-338.
-
(1999)
Periodicum Biologorum
, vol.101
, pp. 333-338
-
-
Gromiha, M.M.1
Selvaraj, S.2
-
70
-
-
0004741713
-
Inter-residue interactions in protein structures
-
Selvaraj S, Gromiha MM, (2000) Inter-residue interactions in protein structures. Current Science 78: 129-131.
-
(2000)
Current Science
, vol.78
, pp. 129-131
-
-
Selvaraj, S.1
Gromiha, M.M.2
-
71
-
-
0033521194
-
First principles prediction of protein folding rates
-
Debe DA, Goddard WA, (1999) First principles prediction of protein folding rates. Journal of Molecular Biology 294: 619-625.
-
(1999)
Journal of Molecular Biology
, vol.294
, pp. 619-625
-
-
Debe, D.A.1
Goddard, W.A.2
-
72
-
-
0032979568
-
Importance of long-range interactions in protein folding
-
Gromiha MM, Selvaraj S, (1999) Importance of long-range interactions in protein folding. Biophysical Chemistry 77: 49-68.
-
(1999)
Biophysical Chemistry
, vol.77
, pp. 49-68
-
-
Gromiha, M.M.1
Selvaraj, S.2
-
73
-
-
0035876847
-
Important inter-residue contacts for enhancing the thermal stability of thermophilic proteins
-
Gromiha MM, (2001) Important inter-residue contacts for enhancing the thermal stability of thermophilic proteins. Biophysical Chemistry 91: 71-77.
-
(2001)
Biophysical Chemistry
, vol.91
, pp. 71-77
-
-
Gromiha, M.M.1
-
74
-
-
0346057951
-
Small-world communication of residues and significance for protein dynamics
-
Atilgan AR, Akan P, Baysal C, (2004) Small-world communication of residues and significance for protein dynamics. Biophysical Journal 86: 85-91.
-
(2004)
Biophysical Journal
, vol.86
, pp. 85-91
-
-
Atilgan, A.R.1
Akan, P.2
Baysal, C.3
-
75
-
-
0037199968
-
Hierarchical organization of modularity in metabolic networks
-
Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL, (2002) Hierarchical organization of modularity in metabolic networks. Science 297: 1551-1555.
-
(2002)
Science
, vol.297
, pp. 1551-1555
-
-
Ravasz, E.1
Somera, A.L.2
Mongru, D.A.3
Oltvai, Z.N.4
Barabasi, A.L.5
-
76
-
-
0028258819
-
Different Sequence Environments of Amino-Acid-Residues Involved and Not Involved in Long-Range Interactions in Proteins
-
Tudos E, Fiser A, Simon I, (1994) Different Sequence Environments of Amino-Acid-Residues Involved and Not Involved in Long-Range Interactions in Proteins. International Journal of Peptide and Protein Research 43: 205-208.
-
(1994)
International Journal of Peptide and Protein Research
, vol.43
, pp. 205-208
-
-
Tudos, E.1
Fiser, A.2
Simon, I.3
-
77
-
-
49749137012
-
Analysis of protein folds using protein contact networks
-
Barah P, Sinha S, (2008) Analysis of protein folds using protein contact networks. Pramana-Journal of Physics 71: 369-378.
-
(2008)
Pramana-Journal of Physics
, vol.71
, pp. 369-378
-
-
Barah, P.1
Sinha, S.2
-
78
-
-
68149141470
-
Protein elastic network models and the ranges of cooperativity
-
Yang L, Song G, Jernigan RL, (2009) Protein elastic network models and the ranges of cooperativity. Proc Natl Acad Sci U S A 106: 12347-12352.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 12347-12352
-
-
Yang, L.1
Song, G.2
Jernigan, R.L.3
-
80
-
-
34249910312
-
Network analysis of protein dynamics
-
Bode C, Kovacs IA, Szalay MS, Palotai R, Korcsmaros T, et al. (2007) Network analysis of protein dynamics. FEBS Letters 581: 2776-2782.
-
(2007)
FEBS Letters
, vol.581
, pp. 2776-2782
-
-
Bode, C.1
Kovacs, I.A.2
Szalay, M.S.3
Palotai, R.4
Korcsmaros, T.5
-
81
-
-
41949141017
-
Proteins as networks: Usefulness of graph theory in protein science
-
Krishnan A, Zbilut JP, Tomita M, Giuliani A, (2008) Proteins as networks: Usefulness of graph theory in protein science. Current Protein & Peptide Science 9: 28-38.
-
(2008)
Current Protein & Peptide Science
, vol.9
, pp. 28-38
-
-
Krishnan, A.1
Zbilut, J.P.2
Tomita, M.3
Giuliani, A.4
-
82
-
-
0014885326
-
Studies on the conformation of amino acids. XI. Analysis of the observed side group conformation in proteins
-
Chandrasekaran R, Ramachandran GN, (1970) Studies on the conformation of amino acids. XI. Analysis of the observed side group conformation in proteins. Int J Protein Res 2: 223-233.
-
(1970)
Int J Protein Res
, vol.2
, pp. 223-233
-
-
Chandrasekaran, R.1
Ramachandran, G.N.2
-
83
-
-
0014723721
-
Backbone and side-chain conformations of amino acids and amino acid residues in peptides
-
Sasisekharan V, Ponnuswamy PK, (1970) Backbone and side-chain conformations of amino acids and amino acid residues in peptides. Biopolymers 9: 1249-1256.
-
(1970)
Biopolymers
, vol.9
, pp. 1249-1256
-
-
Sasisekharan, V.1
Ponnuswamy, P.K.2
-
84
-
-
51849178047
-
Light and electron microscopy studies on brain tissue changes in acute experimental oxygen intoxication
-
von Schnakenburg K, (1971) [Light and electron microscopy studies on brain tissue changes in acute experimental oxygen intoxication]. Virchows Arch B Cell Pathol 8: 230-242.
-
(1971)
Virchows Arch B Cell Pathol
, vol.8
, pp. 230-242
-
-
von Schnakenburg, K.1
-
85
-
-
0018115846
-
Conformation of amino acid side-chains in proteins
-
Janin J, Wodak S, (1978) Conformation of amino acid side-chains in proteins. J Mol Biol 125: 357-386.
-
(1978)
J Mol Biol
, vol.125
, pp. 357-386
-
-
Janin, J.1
Wodak, S.2
-
87
-
-
0020787793
-
Statistical and energetic analysis of side-chain conformations in oligopeptides
-
Benedetti E, Morelli G, Nemethy G, Scheraga HA, (1983) Statistical and energetic analysis of side-chain conformations in oligopeptides. Int J Pept Protein Res 22: 1-15.
-
(1983)
Int J Pept Protein Res
, vol.22
, pp. 1-15
-
-
Benedetti, E.1
Morelli, G.2
Nemethy, G.3
Scheraga, H.A.4
-
88
-
-
0020685129
-
Structure and refinement of penicillopepsin at 1.8 A resolution
-
James MN, Sielecki AR, (1983) Structure and refinement of penicillopepsin at 1.8 A resolution. J Mol Biol 163: 299-361.
-
(1983)
J Mol Biol
, vol.163
, pp. 299-361
-
-
James, M.N.1
Sielecki, A.R.2
-
89
-
-
0023155210
-
Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes
-
Ponder JW, Richards FM, (1987) Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol 193: 775-791.
-
(1987)
J Mol Biol
, vol.193
, pp. 775-791
-
-
Ponder, J.W.1
Richards, F.M.2
-
90
-
-
0034663722
-
The penultimate rotamer library
-
Lovell SC, Word JM, Richardson JS, Richardson DC, (2000) The penultimate rotamer library. Proteins-Structure Function and Genetics 40: 389-408.
-
(2000)
Proteins-Structure Function and Genetics
, vol.40
, pp. 389-408
-
-
Lovell, S.C.1
Word, J.M.2
Richardson, J.S.3
Richardson, D.C.4
-
91
-
-
74549178560
-
MolProbity: all-atom structure validation for macromolecular crystallography
-
Richardson DC, Chen VB, Arendall WB, Headd JJ, Keedy DA, et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica Section D-Biological Crystallography 66: 12-21.
-
(2010)
Acta Crystallographica Section D-Biological Crystallography
, vol.66
, pp. 12-21
-
-
Richardson, D.C.1
Chen, V.B.2
Arendall, W.B.3
Headd, J.J.4
Keedy, D.A.5
-
92
-
-
79955711016
-
-
MATLAB: An Introduction with Applications 2nd Edition: John Wiley & Sons
-
Gilat A, (2004) MATLAB: An Introduction with Applications 2nd Edition: John Wiley & Sons.
-
(2004)
-
-
Gilat, A.1
-
93
-
-
77956150816
-
Understanding on the Residue Contact Network Using the Log-Normal Cluster Model and the Multilevel Wheel Diagram
-
Sun W, He J, (2010) Understanding on the Residue Contact Network Using the Log-Normal Cluster Model and the Multilevel Wheel Diagram. Biopolymers 93: 904-916.
-
(2010)
Biopolymers
, vol.93
, pp. 904-916
-
-
Sun, W.1
He, J.2
-
94
-
-
0035393775
-
An algebraic condition for the separation of two ellipsoids
-
Wang W, Wang J, Kim M-S, (2001) An algebraic condition for the separation of two ellipsoids. Comput Aided Geom Des 18: 531-539.
-
(2001)
Comput Aided Geom Des
, vol.18
, pp. 531-539
-
-
Wang, W.1
Wang, J.2
Kim, M.-S.3
-
95
-
-
2542418133
-
Efficient collision detection for moving ellipsoids using separating planes
-
Wang W, Choi Y-K, Chan B, Kim M-S, Wang J, (2004) Efficient collision detection for moving ellipsoids using separating planes. Computing 72: 235-246.
-
(2004)
Computing
, vol.72
, pp. 235-246
-
-
Wang, W.1
Choi, Y.-K.2
Chan, B.3
Kim, M.-S.4
Wang, J.5
-
96
-
-
72849129457
-
Effect of sidechain anisotropy on residue contact determination
-
In: Chen J, Reddy CK, Chen X, Ruan J, Ely J, editors, 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops; 2009 Nov; Washington D.C, USA
-
Sun W, He J, (2009) Effect of sidechain anisotropy on residue contact determination. In: Chen J, Reddy CK, Chen X, Ruan J, Ely J, editors. pp. 181-188 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops; 2009 Nov; Washington D.C, USA.
-
(2009)
, pp. 181-188
-
-
Sun, W.1
He, J.2
-
97
-
-
38049051121
-
OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing
-
Lu M, Dousis AD, Ma J, (2008) OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing. J Mol Biol 376: 288-301.
-
(2008)
J Mol Biol
, vol.376
, pp. 288-301
-
-
Lu, M.1
Dousis, A.D.2
Ma, J.3
-
98
-
-
34249904389
-
Best-fit ellipsoids of atom-probe tomographic data to study coalescence of gamma' (L1(2)) precipitates in Ni-Al-Cr
-
Karnesky RA, Sudbrack CK, Seidman DN, (2007) Best-fit ellipsoids of atom-probe tomographic data to study coalescence of gamma' (L1(2)) precipitates in Ni-Al-Cr. Scripta Materialia 57: 353-356.
-
(2007)
Scripta Materialia
, vol.57
, pp. 353-356
-
-
Karnesky, R.A.1
Sudbrack, C.K.2
Seidman, D.N.3
-
99
-
-
79955731904
-
-
Physical Properties of Crystals: Their Representation by Tensors and Matrices: Oxford University Press
-
Nye JF, (1985) Physical Properties of Crystals: Their Representation by Tensors and Matrices: Oxford University Press.
-
(1985)
-
-
Nye, J.F.1
|