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Research Article

Protein-Protein Interfaces: Architectures and Interactions in Protein-Protein Interfaces and in Protein Cores. Their Similarities and Differences

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Pages 127-152 | Published online: 26 Sep 2008

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Crossref
Patrick Chène. 2007. Chemical Biology. Chemical Biology 979 1002 .
Gustavo Fenalti, Christiane S. Hampe, Karen O’Connor, J. Paul Banga, Ian R. Mackay, Merrill J. Rowley & Ossama El-Kabbani. (2007) Molecular characterization of a disease associated conformational epitope on GAD65 recognised by a human monoclonal antibody b96.11. Molecular Immunology 44:6, pages 1178-1189.
Crossref
Joan Teyra, Andreas Doms, Michael Schroeder & M Teresa Pisabarro. (2006) SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces. BMC Bioinformatics 7:1.
Crossref
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Crossref
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Crossref
Luckner G. Ulysse & Jean Chmielewski. (2006) A Light-Activated beta-Turn Scaffold within a Somatostatin Analog: NMR Structure and Biological Activity. Chemical Biology <html_ent glyph="@amp;" ascii="&"/> Drug Design 67:2, pages 127-136.
Crossref
Philipp Heuser, Davide Baù, Pascal Benkert & Dietmar Schomburg. (2005) Refinement of unbound protein docking studies using biological knowledge. Proteins: Structure, Function, and Bioinformatics 61:4, pages 1059-1067.
Crossref
Sam Ansari & Volkhard Helms. (2005) Statistical analysis of predominantly transient protein-protein interfaces. Proteins: Structure, Function, and Bioinformatics 61:2, pages 344-355.
Crossref
Shira Mintz, Alexandra Shulman-Peleg, Haim J. Wolfson & Ruth Nussinov. (2005) Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions. Proteins: Structure, Function, and Bioinformatics 61:1, pages 6-20.
Crossref
Dmitry Korkin, Fred P. Davis & Andrej Sali. (2005) Localization of protein-binding sites within families of proteins. Protein Science 14:9, pages 2350-2360.
Crossref
Hannes Ponstingl, Thomas Kabir, Denise Gorse & Janet M. Thornton. (2005) Morphological aspects of oligomeric protein structures. Progress in Biophysics and Molecular Biology 89:1, pages 9-35.
Crossref
Tran Trung Tran, Jim McKie, Wim D.F. Meutermans, Gregory T. Bourne, Peter R. Andrews & Mark L. Smythe. (2005) Topological side-chain classification of β-turns: Ideal motifs for peptidomimetic development. Journal of Computer-Aided Molecular Design 19:8, pages 551-566.
Crossref
Antonio del Sol & Paul O'Meara. (2004) Small-world network approach to identify key residues in protein-protein interaction. Proteins: Structure, Function, and Bioinformatics 58:3, pages 672-682.
Crossref
Fabian Glaser, Yossi Rosenberg, Amit Kessel, Tal Pupko & Nir Ben-Tal. (2004) The ConSurf-HSSP database: The mapping of evolutionary conservation among homologs onto PDB structures. Proteins: Structure, Function, and Bioinformatics 58:3, pages 610-617.
Crossref
Garland R. Marshall & Ilya A. Vakser. 2005. Proteomics and Protein-Protein Interactions. Proteomics and Protein-Protein Interactions 115 146 .
Michelle R. Arkin & James A. Wells. (2004) Small-molecule inhibitors of protein–protein interactions: progressing towards the dream. Nature Reviews Drug Discovery 3:4, pages 301-317.
Crossref
Alexander Berchanski & Miriam Eisenstein. (2003) Construction of molecular assemblies via docking: Modeling of tetramers with D2 symmetry. Proteins: Structure, Function, and Genetics 53:4, pages 817-829.
Crossref
S. Mohan, Neeti Sinha & Sandra J. Smith-Gill. (2003) Modeling the Binding Sites of Anti-Hen Egg White Lysozyme Antibodies HyHEL-8 and HyHEL-26: An Insight into the Molecular Basis of Antibody Cross-Reactivity and Specificity. Biophysical Journal 85:5, pages 3221-3236.
Crossref
Sulin Jiang, Andrei Tovchigrechko & Ilya A. Vakser. (2003) The role of geometric complementarity in secondary structure packing: A systematic docking study. Protein Science 12:8, pages 1646-1651.
Crossref
Alexander I. Archakov, Vadim M. Govorun, Alexander V. Dubanov, Yuri D. Ivanov, Alexander V. Veselovsky, Paul Lewi & Paul Janssen. (2003) Protein‐protein interactions as a target for drugs in proteomics. PROTEOMICS 3:4, pages 380-391.
Crossref
Sachdev S. Sidhu, Wayne J. Fairbrother & Kurt Deshayes. (2003) Exploring Protein-Protein Interactions with Phage Display. ChemBioChem 4:1, pages 14-25.
Crossref
A. V. Veselovsky, Yu. D. Ivanov, A. S. Ivanov, A. I. Archakov, P. Lewi & P. Janssen. (2002) Protein–protein interactions: mechanisms and modification by drugs. Journal of Molecular Recognition 15:6, pages 405-422.
Crossref
Frank Eisenhaber & Peer Bork. 2001. Biotechnology Set. Biotechnology Set 43 86 .
Chihyo Park & Kevin Burgess. (2001) Facile Macrocyclizations to β-Turn Mimics with Diverse Structural, Physical, and Conformational Properties. Journal of Combinatorial Chemistry 3:3, pages 257-266.
Crossref
Fabian Glaser, David M. Steinberg, Ilya A. Vakser & Nir Ben-Tal. (2001) Residue frequencies and pairing preferences at protein-protein interfaces. Proteins: Structure, Function, and Genetics 43:2, pages 89-102.
Crossref
Rajesh Vaidya, Gabriel López & José A. López. 2001. Kirk-Othmer Encyclopedia of Chemical Technology. Kirk-Othmer Encyclopedia of Chemical Technology.
Nathalie Germain, Karine Mérienne, Sophie Zinn-Justin, Jean-Claude Boulain, Frédéric Ducancel & André Ménez. (2000) Molecular and Structural Basis of the Specificity of a Neutralizing Acetylcholine Receptor-mimicking Antibody, Using Combined Mutational and Molecular Modeling Analyses. Journal of Biological Chemistry 275:28, pages 21578-21586.
Crossref
Variath Prasanna, B. Gopal, M.R.N. Murthy, Daniel V. Santi & Padmanabhan Balaram. (1999) Effect of amino acid substitutions at the subunit interface on the stability and aggregation properties of a dimeric protein: Role of Arg 178 and Arg 218 at the dimer interface of thymidylate synthase. Proteins: Structure, Function, and Genetics 34:3, pages 356-368.
Crossref
Chung‐Jung Tsai, Sandeep Kumar, Buyong Ma & Ruth Nussinov. (2008) Folding funnels, binding funnels, and protein function. Protein Science 8:6, pages 1181-1190.
Crossref
Fumin Dong, Stefanie Spott, Olav Zimmermann, Brigitte Kisters-Woike, Benno Müller-Hill & Andrew Barker. (1999) Dimerisation mutants of lac repressor. I. a monomeric mutant, L251A, that binds lac operator DNA as a dimer 1 1Edited by M. Yaniv. Journal of Molecular Biology 290:3, pages 653-666.
Crossref
Frank Eisenhaber & Peer Bork. 1998. Biotechnology. Biotechnology 43 86 .
Chung-Jung Tsai, Dong Xu & Ruth Nussinov. (1998) Protein folding via binding and vice versa. Folding and Design 3:4, pages R71-R80.
Crossref
Teresa A Larsen, Arthur J Olson & David S Goodsell. (1998) Morphology of protein–protein interfaces. Structure 6:4, pages 421-427.
Crossref
Tim Clackson, Mark H. Ultsch, James A. Wells & Abraham M. de Vos. (1998) Structural and functional analysis of the 1:1 growth hormone:receptor complex reveals the molecular basis for receptor affinity. Journal of Molecular Biology 277:5, pages 1111-1128.
Crossref
Yuelin Zhang, Nan-Jun Yu & Linda L. Spremulli. (1998) Mutational Analysis of the Roles of Residues in Escherichia coli Elongation Factor Ts in the Interaction with Elongation Factor Tu. Journal of Biological Chemistry 273:8, pages 4556-4562.
Crossref
Florencio Pazos, Manuela Helmer-Citterich, Gabriele Ausiello & Alfonso Valencia. (1997) Correlated mutations contain information about protein-protein interaction 1 1Edited by A. R. Fersht. Journal of Molecular Biology 271:4, pages 511-523.
Crossref
Chung‐Jung Tsai, Shuo Liang Lin, Haim J. Wolfson & Ruth Nussinov. (2008) Studies of protein‐protein interfaces: A statistical analysis of the hydrophobic effect. Protein Science 6:1, pages 53-64.
Crossref
Ilya A. Vakser. (1997) Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex. Proteins: Structure, Function, and Genetics 29:S1, pages 226-230.
Crossref

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