Modelling repressor proteins docking to DNA

By Patrick Aloy, Gidon Moont, H. Gabb, E. Querol, F. Avilés, Michael J.E. Sternberg. 1998

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1. M. V. van Dijk
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5. V. Tsui
6. Mark Gerstein
7. D. Greenbaum
8. V. Hsu

Citations in the corpus

• What is Bioinformatics? A Proposed Definition and Overview of the Field (2001, methodology): “In a different approach, molecular simulation techniques have been used to dock whole proteins and DNAs on the basis of force-field calculations around the two molecules [68, 69].”
• Information-driven protein–DNA docking using HADDOCK: it is a matter of flexibility (2006, methodology): “The program FTDOCK (9) has been used to perform a large search through conformational space by rotating and translating the protein along the DNA while evaluating shape and electrostatic complementarity; an approximation of flexibility was achieved by allowing some degree of overlap between protein ”
• Predicting interactions of winged‐helix transcription factors with DNA (2004, methodology): “21,22 Using coordinates of the unbound proteins and model B-DNA structures, proteins were docked onto DNA with the program FTDOCK, 23 which ranks solutions by shape complementarity during the search and requires a favorable electrostatic interaction.”