Protein Engineering vol. 8 no. 2 pp. 127-134, 1995
© 1995 Oxford University Press
RESEARCH-ARTICLE |
LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions
Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College, Gower Street, London WC1E 6BT, UK
1To Whom correspondence should be addressed
The LIGPLOT program automatically generates schematic 2-D representations of protein-ligand complexes from standard Protein Data Bank file input The output is a colour, or black-and-white, PostScript file giving a simple and informative representation of the intermolecular interactions and their strengths, including hydrogen bonds, hydrophobic interactions and atom accessibilities. The program is completely general for any ligand and can also be used to show other types of interaction in proteins and nucleic acids. It was designed to facilitate the rapid inspection of many enzyme complexes, but has found many other applications
Keywords: enzyme inhibitors/hydrogen bonding/protein-ligand interactions/software tools
Received September 15, 1994; revised December 6, 1994; accepted December 19, 1994.
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A. M. Wu, T. Singh, J.-H. Liu, M. Krzeminski, R. Russwurm, H.-C. Siebert, A. M.J.J. Bonvin, S. Andre, and H.-J. Gabius Activity-structure correlations in divergent lectin evolution: fine specificity of chicken galectin CG-14 and computational analysis of flexible ligand docking for CG-14 and the closely related CG-16 Glycobiology, February 1, 2007; 17(2): 165 - 184. [Abstract] [Full Text] [PDF]
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M. St. Maurice, P. E. Mera, M. P. Taranto, F. Sesma, J. C. Escalante-Semerena, and I. Rayment Structural Characterization of the Active Site of the PduO-Type ATP:Co(I)rrinoid Adenosyltransferase from Lactobacillus reuteri J. Biol. Chem., January 26, 2007; 282(4): 2596 - 2605. [Abstract] [Full Text] [PDF]
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D. von Stetten, S. Seibeck, N. Michael, P. Scheerer, M. A. Mroginski, D. H. Murgida, N. Krauss, M. P. Heyn, P. Hildebrandt, B. Borucki, et al. Highly Conserved Residues Asp-197 and His-250 in Agp1 Phytochrome Control the Proton Affinity of the Chromophore and Pfr Formation J. Biol. Chem., January 19, 2007; 282(3): 2116 - 2123. [Abstract] [Full Text] [PDF]
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T. Abaffy, A. Malhotra, and C. W. Luetje The Molecular Basis for Ligand Specificity in a Mouse Olfactory Receptor: A NETWORK OF FUNCTIONALLY IMPORTANT RESIDUES J. Biol. Chem., January 12, 2007; 282(2): 1216 - 1224. [Abstract] [Full Text] [PDF]
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P. M. Matias, S. Gorynia, P. Donner, and M. A. Carrondo Crystal Structure of the Human AAA+ Protein RuvBL1 J. Biol. Chem., December 15, 2006; 281(50): 38918 - 38929. [Abstract] [Full Text] [PDF]
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Q. Han, H. Robinson, Y. G. Gao, N. Vogelaar, S. R. Wilson, M. Rizzi, and J. Li Crystal Structures of Aedes aegypti Alanine Glyoxylate Aminotransferase J. Biol. Chem., December 1, 2006; 281(48): 37175 - 37182. [Abstract] [Full Text] [PDF]
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C. C. Marohnic, S. P. Panda, P. Martasek, and B. S. Masters Diminished FAD Binding in the Y459H and V492E Antley-Bixler Syndrome Mutants of Human Cytochrome P450 Reductase J. Biol. Chem., November 24, 2006; 281(47): 35975 - 35982. [Abstract] [Full Text] [PDF]
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J. Zaitseva, J. Lu, K. L. Olechoski, and A. L. Lamb Two Crystal Structures of the Isochorismate Pyruvate Lyase from Pseudomonas aeruginosa J. Biol. Chem., November 3, 2006; 281(44): 33441 - 33449. [Abstract] [Full Text] [PDF]
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E. Seiradake, H. Lortat-Jacob, O. Billet, E. J. Kremer, and S. Cusack Structural and Mutational Analysis of Human Ad37 and Canine Adenovirus 2 Fiber Heads in Complex with the D1 Domain of Coxsackie and Adenovirus Receptor J. Biol. Chem., November 3, 2006; 281(44): 33704 - 33716. [Abstract] [Full Text] [PDF]
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P. P. Knowles, J. Murray-Rust, S. Kjaer, R. P. Scott, S. Hanrahan, M. Santoro, C. F. Ibanez, and N. Q. McDonald Structure and Chemical Inhibition of the RET Tyrosine Kinase Domain J. Biol. Chem., November 3, 2006; 281(44): 33577 - 33587. [Abstract] [Full Text] [PDF]
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S. Nakamura, M. Oda, S. Kataoka, S. Ueda, S. Uchiyama, T. Yoshida, Y. Kobayashi, and T. Ohkubo Apo- and Holo-structures of 3{alpha}-Hydroxysteroid Dehydrogenase from Pseudomonas sp. B-0831: LOOP-HELIX TRANSITION INDUCED BY COENZYME BINDING J. Biol. Chem., October 20, 2006; 281(42): 31876 - 31884. [Abstract] [Full Text] [PDF]
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P. H. C. Godoi, R. S. Galhardo, D. D. Luche, M.-A. Van Sluys, C. F. M. Menck, and G. Oliva Structure of the Thiazole Biosynthetic Enzyme THI1 from Arabidopsis thaliana J. Biol. Chem., October 13, 2006; 281(41): 30957 - 30966. [Abstract] [Full Text] [PDF]
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J. E. Chrencik, A. Brooun, M. L. Kraus, M. I. Recht, A. R. Kolatkar, G. W. Han, J. M. Seifert, H. Widmer, M. Auer, and P. Kuhn Structural and Biophysical Characterization of the EphB4{middle dot}EphrinB2 Protein-Protein Interaction and Receptor Specificity J. Biol. Chem., September 22, 2006; 281(38): 28185 - 28192. [Abstract] [Full Text] [PDF]
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M. Hothorn, A. Wachter, R. Gromes, T. Stuwe, T. Rausch, and K. Scheffzek Structural Basis for the Redox Control of Plant Glutamate Cysteine Ligase J. Biol. Chem., September 15, 2006; 281(37): 27557 - 27565. [Abstract] [Full Text] [PDF]
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A. Addlagatta, L. Gay, and B. W. Matthews Structure of aminopeptidase N from Escherichia coli suggests a compartmentalized, gated active site PNAS, September 5, 2006; 103(36): 13339 - 13344. [Abstract] [Full Text] [PDF]
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S. J. de Vries and A. M. J. J. Bonvin Intramolecular surface contacts contain information about protein-protein interface regions Bioinformatics, September 1, 2006; 22(17): 2094 - 2098. [Abstract] [Full Text] [PDF]
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J.-Y. Hsieh, G.-Y. Liu, G.-G. Chang, and H.-C. Hung Determinants of the Dual Cofactor Specificity and Substrate Cooperativity of the Human Mitochondrial NAD(P)+-dependent Malic Enzyme: FUNCTIONAL ROLES OF GLUTAMINE 362 J. Biol. Chem., August 11, 2006; 281(32): 23237 - 23245. [Abstract] [Full Text] [PDF]
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V.C. Epa and C. W. Ward Model for the complex between the insulin-like growth factor I and its receptor: towards designing antagonists for the IGF-1 receptor Protein Eng. Des. Sel., August 1, 2006; 19(8): 377 - 384. [Abstract] [Full Text] [PDF]
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K. Ito, M. Nakanishi, W.-C. Lee, H. Sasaki, S. Zenno, K. Saigo, Y. Kitade, and M. Tanokura Three-dimensional Structure of AzoR from Escherichia coli: AN OXIDEREDUCTASE CONSERVED IN MICROORGANISMS J. Biol. Chem., July 21, 2006; 281(29): 20567 - 20576. [Abstract] [Full Text] [PDF]
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K. Stierand, P. C. Maass, and M. Rarey Molecular complexes at a glance: automated generation of two-dimensional complex diagrams Bioinformatics, July 15, 2006; 22(14): 1710 - 1716. [Abstract] [Full Text] [PDF]
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M. van Dijk, A. D. J. van Dijk, V. Hsu, R. Boelens, and A. M. J. J. Bonvin Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility Nucleic Acids Res., July 4, 2006; 34(11): 3317 - 3325. [Abstract] [Full Text] [PDF]
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C. Chen, A. K. Saxena, W. N. Simcoke, D. N. Garboczi, P. L. Pedersen, and Y. H. Ko Mitochondrial ATP Synthase: CRYSTAL STRUCTURE OF THE CATALYTIC F1 UNIT IN A VANADATE-INDUCED TRANSITION-LIKE STATE AND IMPLICATIONS FOR MECHANISM J. Biol. Chem., May 12, 2006; 281(19): 13777 - 13783. [Abstract] [Full Text] [PDF]
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L. Du, Z. Zhang, X. Luo, K. Chen, X. Shen, and H. Jiang Binding Investigation of Human 5-Lipoxygenase with Its Inhibitors by SPR Technology Correlating with Molecular Docking Simulation. J. Biochem., April 1, 2006; 139(4): 715 - 723. [Abstract] [Full Text] [PDF]
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