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A systematic study of low-resolution recognition in protein--protein complexes.
Proc Natl Acad Sci U S A. 1999 Jul 20;96(15):8477-82. doi: 10.1073/pnas.96.15.8477.
2
Docking of protein models.
Protein Sci. 2002 Aug;11(8):1888-96. doi: 10.1110/ps.4730102.
3
Shape complementarity of protein-protein complexes at multiple resolutions.
Proteins. 2009 May 1;75(2):453-67. doi: 10.1002/prot.22256.
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Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints.
J Comput Chem. 2008 Jul 30;29(10):1574-88. doi: 10.1002/jcc.20917.
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Global and local structural similarity in protein-protein complexes: implications for template-based docking.
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7
How common is the funnel-like energy landscape in protein-protein interactions?
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8
A simple shape characteristic of protein-protein recognition.
Bioinformatics. 2007 Apr 1;23(7):789-92. doi: 10.1093/bioinformatics/btm018. Epub 2007 Jan 31.
9
Molecular docking studies of protein-nucleotide complexes using MOLSDOCK (mutually orthogonal Latin squares DOCK).
J Mol Model. 2012 Aug;18(8):3705-22. doi: 10.1007/s00894-012-1369-4. Epub 2012 Mar 1.
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Improved FlexX docking using FlexS-determined base fragment placement.
J Chem Inf Model. 2005 Jul-Aug;45(4):993-1001. doi: 10.1021/ci050026f.

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Docking Foundations: From Rigid to Flexible Docking.
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Size of the protein-protein energy funnel in crowded environment.
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Cold spots are universal in protein-protein interactions.
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Chemokine CXCL12 drives pericyte accumulation and airway remodeling in allergic airway disease.
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DOCKGROUND membrane protein-protein set.
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Challenges in protein docking.
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A PRMT5-RNF168-SMURF2 Axis Controls H2AX Proteostasis.
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Inhibition of protein interactions: co-crystalized protein-protein interfaces are nearly as good as holo proteins in rigid-body ligand docking.
J Comput Aided Mol Des. 2018 Jul;32(7):769-779. doi: 10.1007/s10822-018-0124-z. Epub 2018 Jul 12.
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Positive Charges on the Surface of Thaumatin Are Crucial for the Multi-Point Interaction with the Sweet Receptor.
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本文引用的文献

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Free energy landscapes of encounter complexes in protein-protein association.
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A potential smoothing algorithm accurately predicts transmembrane helix packing.
Nat Struct Biol. 1999 Jan;6(1):50-5. doi: 10.1038/4922.
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Large-scale protein structure modeling of the Saccharomyces cerevisiae genome.
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Reaching the global minimum in docking simulations: a Monte Carlo energy minimization approach using Bezier splines.
Proc Natl Acad Sci U S A. 1998 Jul 7;95(14):8011-5. doi: 10.1073/pnas.95.14.8011.
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Identification of the binding site on cytochrome P450 2B4 for cytochrome b5 and cytochrome P450 reductase.
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Predictive docking of protein-protein and protein-DNA complexes.
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