-
2
-
-
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: 235-42.
-
(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
-
3
-
-
0026572775
-
Molecular sur-face recognition: determination of geometric fit between proteins and their ligands by correlation techniques
-
Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aalo C, et al. (1992) Molecular sur-face recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proceedings of the National Academy of Sciences of the United States of America 89: 2195-2199.
-
(1992)
Proceedings of the National Academy of Sciences of the United States of America
, vol.89
, pp. 2195-2199
-
-
Katchalski-Katzir, E.1
Shariv, I.2
Eisenstein, M.3
Friesem, A.A.4
Aalo, C.5
-
4
-
-
0031565730
-
Modelling protein docking using shape complemen-tarity, electrostatics and biochemical information
-
Gabb HA, Jackson RM, Sternberg MJE, (1997) Modelling protein docking using shape complemen-tarity, electrostatics and biochemical information. Journal of Molecular Biology 272: 106-120.
-
(1997)
Journal of Molecular Biology
, vol.272
, pp. 106-120
-
-
Gabb, H.A.1
Jackson, R.M.2
Sternberg, M.J.E.3
-
5
-
-
0034193510
-
Protein docking using spherical polar Fourier correlations
-
Ritchie DW, Kemp GJ, (2000) Protein docking using spherical polar Fourier correlations. Proteins: Structure, Function, and Genetics 39: 178-194.
-
(2000)
Proteins: Structure, Function, and Genetics
, vol.39
, pp. 178-194
-
-
Ritchie, D.W.1
Kemp, G.J.2
-
6
-
-
13344261720
-
-
Phd thesis, Departments of Computer Science & Molecular and Cell Biology, University of Aberdeen, King's College, Aberdeen, UK
-
Ritchie DW (1998) Parametric Protein Shape Recognition. Phd thesis, Departments of Computer Science & Molecular and Cell Biology, University of Aberdeen, King's College, Aberdeen, UK.
-
(1998)
Parametric Protein Shape Recognition
-
-
Ritchie, D.W.1
-
7
-
-
0027551946
-
Approximation and characterization of molecular surfaces
-
Duncan BS, Olson AJ, (1993) Approximation and characterization of molecular surfaces. Biopoly-mers 33: 219-229.
-
(1993)
Biopoly-Mers
, vol.33
, pp. 219-229
-
-
Duncan, B.S.1
Olson, A.J.2
-
9
-
-
0041566879
-
Fast rotational matching of rigid bodies by fast fourier transform acceleration of five degrees of freedom
-
Kovacs JA, Chacon P, Cong Y, Metwally E, Wriggers W, (2003) Fast rotational matching of rigid bodies by fast fourier transform acceleration of five degrees of freedom. Acta Crystallographica, Biological Crystallography D59: 1371-1376.
-
(2003)
Acta Crystallographica, Biological Crystallography
, vol.D59
, pp. 1371-1376
-
-
Kovacs, J.A.1
Chacon, P.2
Cong, Y.3
Metwally, E.4
Wriggers, W.5
-
10
-
-
73149111493
-
Simultaneous prediction of protein folding and docking at high resolution
-
Das R, Andre I, Shen Y, Wu Y, Lemak A, et al. (2009) Simultaneous prediction of protein folding and docking at high resolution. Proceedings of the National Academy of Sciences of the United States of America 106: 18978-18983.
-
(2009)
Proceedings of the National Academy of Sciences of the United States of America
, vol.106
, pp. 18978-18983
-
-
Das, R.1
Andre, I.2
Shen, Y.3
Wu, Y.4
Lemak, A.5
-
11
-
-
0037442962
-
Haddock: a protein-protein docking approach based on biochemical or biophysical information
-
Dominguez C, Boelens R, Bonvin AMJJ, (2003) Haddock: a protein-protein docking approach based on biochemical or biophysical information. Journal of the American Chemical Society 125: 1731-1737.
-
(2003)
Journal of the American Chemical Society
, vol.125
, pp. 1731-1737
-
-
Dominguez, C.1
Boelens, R.2
Bonvin, A.M.J.J.3
-
12
-
-
84856772706
-
Optimized grid-based protein-protein docking as a global search tool followed by incorporating experimentally derivable restraints
-
Huang W, Liu H, (2012) Optimized grid-based protein-protein docking as a global search tool followed by incorporating experimentally derivable restraints. Proteins 80: 691-702.
-
(2012)
Proteins
, vol.80
, pp. 691-702
-
-
Huang, W.1
Liu, H.2
-
13
-
-
0038185277
-
A novel shape complementarity scoring function for protein-protein dock-ing
-
Chen R, Weng Z, (2003) A novel shape complementarity scoring function for protein-protein dock-ing. Proteins: Structure, Function, and Genetics 51: 397-408.
-
(2003)
Proteins: Structure, Function, and Genetics
, vol.51
, pp. 397-408
-
-
Chen, R.1
Weng, Z.2
-
14
-
-
83555176324
-
Surface-histogram: A new shape descriptor for protein-protein docking
-
Gu S, Koehl P, Hass J, Amenta N, (2012) Surface-histogram: A new shape descriptor for protein-protein docking. Proteins: Structure, Function, and Bioinformatics 80: 221-238.
-
(2012)
Proteins: Structure, Function, and Bioinformatics
, vol.80
, pp. 221-238
-
-
Gu, S.1
Koehl, P.2
Hass, J.3
Amenta, N.4
-
15
-
-
0035040480
-
Protein docking using continuum electrostatics and geometric fit
-
Mandell JG, Roberts VA, Pique ME, Kotlovyi V, Mitchell JC, et al. (2001) Protein docking using continuum electrostatics and geometric fit. Protein Engineering 14: 105-113.
-
(2001)
Protein Engineering
, vol.14
, pp. 105-113
-
-
Mandell, J.G.1
Roberts, V.A.2
Pique, M.E.3
Kotlovyi, V.4
Mitchell, J.C.5
-
16
-
-
0037093643
-
Docking unbound proteins using shape complementarity, desolvation, and electrostatics
-
Chen R, Weng Z, (2002) Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins: Structure, Function, and Genetics 47: 281-294.
-
(2002)
Proteins: Structure, Function, and Genetics
, vol.47
, pp. 281-294
-
-
Chen, R.1
Weng, Z.2
-
17
-
-
33749020839
-
PIPER: An FFT-based protein docking program with pairwise potentials
-
Kozakov D, Brenke R, Comeau S, Vajda S, (2006) PIPER: An FFT-based protein docking program with pairwise potentials. Proteins: Structure, Function, and Bioinformatics 65: 392-406.
-
(2006)
Proteins: Structure, Function, and Bioinformatics
, vol.65
, pp. 392-406
-
-
Kozakov, D.1
Brenke, R.2
Comeau, S.3
Vajda, S.4
-
18
-
-
0038187616
-
Weighted geometric docking: incorporating external information in the rotation-translation scan
-
Ben-Zeev E, Eisenstein M, (2003) Weighted geometric docking: incorporating external information in the rotation-translation scan. Proteins: Structure, Function, and Bioinformatics 52: 24-27.
-
(2003)
Proteins: Structure, Function, and Bioinformatics
, vol.52
, pp. 24-27
-
-
Ben-Zeev, E.1
Eisenstein, M.2
-
19
-
-
0037849892
-
Prediction of the unknown: Inspiring experience with the CAPRI experiment
-
Ben-Zeev E, Berchanski A, Heifetz A, Shapira B, Eisenstein M, (2003) Prediction of the unknown: Inspiring experience with the CAPRI experiment. Proteins: Structure, Function, and Bioinformatics 52: 41-46.
-
(2003)
Proteins: Structure, Function, and Bioinformatics
, vol.52
, pp. 41-46
-
-
Ben-Zeev, E.1
Berchanski, A.2
Heifetz, A.3
Shapira, B.4
Eisenstein, M.5
-
20
-
-
0242299200
-
Rdock: Refinement of rigid-body protein docking predictions
-
Li L, Chen R, Weng Z, (2003) Rdock: Refinement of rigid-body protein docking predictions. Pro-teins: Structure, Function, and Genetics 53: 693-707.
-
(2003)
Pro-Teins: Structure, Function, and Genetics
, vol.53
, pp. 693-707
-
-
Li, L.1
Chen, R.2
Weng, Z.3
-
21
-
-
35449008122
-
Integrating statistical pair potentials into protein complex prediction
-
Mintseris J, Pierce B, Wiehe K, Anderson R, Chen R, et al. (2007) Integrating statistical pair potentials into protein complex prediction. Proteins: Structure, Function, and Bioinformatics 69: 511-520.
-
(2007)
Proteins: Structure, Function, and Bioinformatics
, vol.69
, pp. 511-520
-
-
Mintseris, J.1
Pierce, B.2
Wiehe, K.3
Anderson, R.4
Chen, R.5
-
22
-
-
70349882144
-
FRODOCK: a new approach for fast rotational protein-protein docking
-
Garzon J, Lopez-Blanco J, Pons C, Kovacs J, Abagyan R, et al. (2009) FRODOCK: a new approach for fast rotational protein-protein docking. Bioinformatics 25: 2544-2551.
-
(2009)
Bioinformatics
, vol.25
, pp. 2544-2551
-
-
Garzon, J.1
Lopez-Blanco, J.2
Pons, C.3
Kovacs, J.4
Abagyan, R.5
-
23
-
-
77449134208
-
Pie - efficient filters and coarse grained potentials for unbound protein-protein docking
-
Ravikant DVS, Elber R, (2010) Pie- efficient filters and coarse grained potentials for unbound protein-protein docking. Proteins 78: 400-419.
-
(2010)
Proteins
, vol.78
, pp. 400-419
-
-
Ravikant, D.V.S.1
Elber, R.2
-
24
-
-
79960036791
-
DECK: Distance and environment-dependent, coarse-grained, knowledge- based potentials for protein-protein docking
-
Liu S, Vakser IA (2011) DECK: Distance and environment-dependent, coarse-grained, knowledge- based potentials for protein-protein docking. BMC Bioinformatics 12.
-
(2011)
BMC Bioinformatics 12
-
-
Liu, S.1
Vakser, I.A.2
-
25
-
-
41949111630
-
Recent progress and future directions in protein-protein docking
-
Ritchie D, (2008) Recent progress and future directions in protein-protein docking. Current Protein and Peptide Science 9: 1-15.
-
(2008)
Current Protein and Peptide Science
, vol.9
, pp. 1-15
-
-
Ritchie, D.1
-
27
-
-
33646472024
-
High-resolution protein-protein docking
-
Gray J, (2006) High-resolution protein-protein docking. Current opinion in structural biology 16: 183-193.
-
(2006)
Current Opinion in Structural Biology
, vol.16
, pp. 183-193
-
-
Gray, J.1
-
29
-
-
0036606483
-
Principles of docking: an overview of search algorithms and a guide to scoring functions
-
Halperin I, Ma B, Wolfson H, Nussinov R, (2002) Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins: Structure, Function, and Bioinformatics 47: 409-443.
-
(2002)
Proteins: Structure, Function, and Bioinformatics
, vol.47
, pp. 409-443
-
-
Halperin, I.1
Ma, B.2
Wolfson, H.3
Nussinov, R.4
-
33
-
-
78650553291
-
A dynamic data structure for flexible molecular maintenance and informatics
-
Bajaj C, Chowdhury RA, Rasheed M, (2010) A dynamic data structure for flexible molecular maintenance and informatics. Bioinformatics 27: 55-62.
-
(2010)
Bioinformatics
, vol.27
, pp. 55-62
-
-
Bajaj, C.1
Chowdhury, R.A.2
Rasheed, M.3
-
34
-
-
77958035118
-
Fast molecular solvation energetics and forces computation
-
Bajaj C, (2010) ZhaoW (2010) Fast molecular solvation energetics and forces computation. SIAM Journal on Scientific Computing 31: 4524-4552.
-
(2010)
SIAM Journal on Scientific Computing
, vol.31
, pp. 4524-4552
-
-
Bajaj, C.1
Zhao, W.2
-
36
-
-
21644480883
-
Protein-protein docking bench-mark 2.0: an update
-
Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, et al. (2003) Protein-protein docking bench-mark 2.0: an update. Proteins 60: 214-6.
-
(2003)
Proteins
, vol.60
, pp. 214-216
-
-
Mintseris, J.1
Wiehe, K.2
Pierce, B.3
Anderson, R.4
Chen, R.5
-
37
-
-
77957944014
-
Protein-protein docking benchmark version 4.0
-
Hwang H, Vreven T, Janin J, Weng Z, (2010) Protein-protein docking benchmark version 4.0. Proteins: Structure, Function, and Bioinformatics 78: 3111-3114.
-
(2010)
Proteins: Structure, Function, and Bioinformatics
, vol.78
, pp. 3111-3114
-
-
Hwang, H.1
Vreven, T.2
Janin, J.3
Weng, Z.4
-
38
-
-
55549101290
-
Sampling rotation groups by successive orthogonal images
-
Mitchell JC, (2008) Sampling rotation groups by successive orthogonal images. SIAM Journal on Scientific Computing 30: 525-547.
-
(2008)
SIAM Journal on Scientific Computing
, vol.30
, pp. 525-547
-
-
Mitchell, J.C.1
-
39
-
-
0001482877
-
Optimal sampling of the rotation function
-
Lattman EE, (1972) Optimal sampling of the rotation function. Acta Crystallographica Section B 28: 1065-1068.
-
(1972)
Acta Crystallographica Section B
, vol.28
, pp. 1065-1068
-
-
Lattman, E.E.1
-
40
-
-
20744449792
-
The design and implementation of FFTW3
-
Frigo M, Johnson SG, (2005) The design and implementation of FFTW3. Proceedings of the IEEE Invited paper, Special Issue on Program Generation, Optimization, and Platform Adaptation 93: 216-231.
-
(2005)
Proceedings of the IEEE Invited Paper, Special Issue on Program Generation, Optimization, and Platform Adaptation
, vol.93
, pp. 216-231
-
-
Frigo, M.1
Johnson, S.G.2
-
41
-
-
84986532964
-
Grid-search molecular accessible surface algorithm for solving the protein docking problem
-
Wang H, (1991) Grid-search molecular accessible surface algorithm for solving the protein docking problem. Journal of Computational Chemistry 12: 746-750.
-
(1991)
Journal of Computational Chemistry
, vol.12
, pp. 746-750
-
-
Wang, H.1
-
42
-
-
0031565729
-
Analysis of protein-protein interaction sites using surface patches
-
Jones S, Thornton JM, (1997) Analysis of protein-protein interaction sites using surface patches. Journal of Molecular Biology 272: 121-132.
-
(1997)
Journal of Molecular Biology
, vol.272
, pp. 121-132
-
-
Jones, S.1
Thornton, J.M.2
-
44
-
-
0035342450
-
Residue frequencies and pairing preferences at protein-protein interfaces
-
Glaser F, Steinberg DM, Vakser IA, Ben-Tal N, (2001) Residue frequencies and pairing preferences at protein-protein interfaces. Proteins: Structure, Function, and Genetics 43: 89-102.
-
(2001)
Proteins: Structure, Function, and Genetics
, vol.43
, pp. 89-102
-
-
Glaser, F.1
Steinberg, D.M.2
Vakser, I.A.3
Ben-Tal, N.4
-
45
-
-
0021757436
-
A new force field for molecular mechanical simulation of nucleic acids and proteins
-
Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, et al. (1984) A new force field for molecular mechanical simulation of nucleic acids and proteins. Journal of the American Chemical Society 106: 765-784.
-
(1984)
Journal of the American Chemical Society
, vol.106
, pp. 765-784
-
-
Weiner, S.J.1
Kollman, P.A.2
Case, D.A.3
Singh, U.C.4
Ghio, C.5
-
46
-
-
0030203710
-
Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4
-
Morris GM, Goodsell DS, Huey R, Olson AJ, (1996) Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4. Journal of Computer-Aided Molecular Design 10: 293-304.
-
(1996)
Journal of Computer-Aided Molecular Design
, vol.10
, pp. 293-304
-
-
Morris, G.M.1
Goodsell, D.S.2
Huey, R.3
Olson, A.J.4
-
47
-
-
0000390128
-
Glycine residues provide exibility for enzyme active sites
-
Yan B, Sun Y, (1997) Glycine residues provide exibility for enzyme active sites. Journal of Bio-logical Chemistry 272: 3190.
-
(1997)
Journal of Bio-Logical Chemistry
, vol.272
, pp. 3190
-
-
Yan, B.1
Sun, Y.2
-
48
-
-
0030580057
-
Antibody-antigen interactions: contact analysis and binding site topography
-
MacCallum R, Martin A, Thornton J, (1996) Antibody-antigen interactions: contact analysis and binding site topography. Journal of Molecular Biology 262: 732-745.
-
(1996)
Journal of Molecular Biology
, vol.262
, pp. 732-745
-
-
MacCallum, R.1
Martin, A.2
Thornton, J.3
-
49
-
-
79957860276
-
Protein sequence and structure analysis of antibody variable domains
-
Martin A (2010) Protein sequence and structure analysis of antibody variable domains. Antibody engineering: 33-51.
-
(2010)
Antibody engineering
, pp. 33-51
-
-
Martin, A.1
-
51
-
-
0022596727
-
Solvation energy in protein folding and binding
-
Eisenberg D, Mclachlan A, (1986) Solvation energy in protein folding and binding. Nature 319: 199-203.
-
(1986)
Nature
, vol.319
, pp. 199-203
-
-
Eisenberg, D.1
McLachlan, A.2
-
52
-
-
0001585447
-
Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation
-
Gilson M, Davis M, Luty B, McCammon J, (1993) Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation. Journal of Physical Chemistry 97: 3591-3600.
-
(1993)
Journal of Physical Chemistry
, vol.97
, pp. 3591-3600
-
-
Gilson, M.1
Davis, M.2
Luty, B.3
McCammon, J.4
-
53
-
-
0011930746
-
Theory of hydrophobic bonding. ii. correlation of hydrocarbon solubility in water with solvent cavity surface area
-
Hermann RB, (1972) Theory of hydrophobic bonding. ii. correlation of hydrocarbon solubility in water with solvent cavity surface area. Journal of Physical Chemistry 76: 2754-2759.
-
(1972)
Journal of Physical Chemistry
, vol.76
, pp. 2754-2759
-
-
Hermann, R.B.1
-
54
-
-
84986430566
-
Incorporating solvent and ion screening into molecular dynamics using the finite-difference poisson-boltzmann method
-
Sharp K, (1991) Incorporating solvent and ion screening into molecular dynamics using the finite-difference poisson-boltzmann method. Journal of Computational Chemistry 12: 454-468.
-
(1991)
Journal of Computational Chemistry
, vol.12
, pp. 454-468
-
-
Sharp, K.1
-
55
-
-
0000831520
-
Solvation free energies estimated from macroscopic continuum theory: An accuracy assessment
-
Simonson T, Bruenger AT, (1994) Solvation free energies estimated from macroscopic continuum theory: An accuracy assessment. Journal of Physical Chemistry 98: 4683-4694.
-
(1994)
Journal of Physical Chemistry
, vol.98
, pp. 4683-4694
-
-
Simonson, T.1
Bruenger, A.T.2
-
56
-
-
33744822783
-
Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms
-
Wagoner J, Baker N, (2006) Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms. Proceesings of the National Academy of Sciences of the USA 103: 8331-8336.
-
(2006)
Proceesings of the National Academy of Sciences of the USA
, vol.103
, pp. 8331-8336
-
-
Wagoner, J.1
Baker, N.2
-
57
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still WC, Tempczyk A, Hawley RC, Hendrickson T, (1990) Semianalytical treatment of solvation for molecular mechanics and dynamics. Journal of the American Chemical Society 112: 6127-6129.
-
(1990)
Journal of the American Chemical Society
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
58
-
-
3242886771
-
PDB2PQR: An automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations
-
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA, (2004) PDB2PQR: An automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research 32: w665-w667.
-
(2004)
Nucleic Acids Research
, vol.32
-
-
Dolinsky, T.J.1
Nielsen, J.E.2
McCammon, J.A.3
Baker, N.A.4
-
59
-
-
0242663237
-
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
-
Duan Y, Wu C, Chowdhury S, Lee M, Xiong G, et al. (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry 24: 1999-2012.
-
(2003)
Journal of Computational Chemistry
, vol.24
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
Chowdhury, S.3
Lee, M.4
Xiong, G.5
-
60
-
-
0037189507
-
Three camelid vhh domains in complex with porcine pancreatic alpha-amylase. inhibition and versatility of binding topology
-
Desmyter A, Spinelli S, Payan F, Lauwereys M, Wyns L, et al. (2002) Three camelid vhh domains in complex with porcine pancreatic alpha-amylase. inhibition and versatility of binding topology. Journal of Biological Chemistry 277: 23645-23650.
-
(2002)
Journal of Biological Chemistry
, vol.277
, pp. 23645-23650
-
-
Desmyter, A.1
Spinelli, S.2
Payan, F.3
Lauwereys, M.4
Wyns, L.5
-
61
-
-
80052903046
-
Accelerating protein docking in ZDOCK using an advanced 3d convolution library
-
Pierce BG, Hourai Y, Weng Z, (2011) Accelerating protein docking in ZDOCK using an advanced 3d convolution library. PLoS ONE 6: e24657.
-
(2011)
PLoS ONE
, vol.6
-
-
Pierce, B.G.1
Hourai, Y.2
Weng, Z.3
-
62
-
-
0038359614
-
CAPRI: A Critical Assessment of PRedicted Interactions
-
Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJE, et al. (2003) CAPRI: A Critical Assessment of PRedicted Interactions. Proteins 52: 2-9.
-
(2003)
Proteins
, vol.52
, pp. 2-9
-
-
Janin, J.1
Henrick, K.2
Moult, J.3
Eyck, L.T.4
Sternberg, M.J.E.5
-
63
-
-
34548317146
-
FireDock: fast interaction refinement in molecular docking
-
Andrusier N, Nussinov R, Wolfson H, (2007) FireDock: fast interaction refinement in molecular docking. Proteins 69: 139-159.
-
(2007)
Proteins
, vol.69
, pp. 139-159
-
-
Andrusier, N.1
Nussinov, R.2
Wolfson, H.3
-
64
-
-
0042511005
-
A graph-theory algorithm for rapid protein side-chain prediction
-
Canutescu A, Shelenkov A, Dunbrack Jr R, (2003) A graph-theory algorithm for rapid protein side-chain prediction. Protein Science 12: 2001-2014.
-
(2003)
Protein Science
, vol.12
, pp. 2001-2014
-
-
Canutescu, A.1
Shelenkov, A.2
Dunbrack Jr, R.3
|