Sampling the conformation of protein surface residues for flexible protein docking |
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Authors: | Patricia Francis-Lyon Shengyin Gu Joel Hass Nina Amenta Patrice Koehl |
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Institution: | 1.Department of Computer Science,University of California,Davis,USA;2.Department of Mathematics,University of California,Davis,USA;3.Department of Computer Science and Genome Center,University of California,Davis,USA |
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Abstract: | Background The problem of determining the physical conformation of a protein dimer, given the structures of the two interacting proteins
in their unbound state, is a difficult one. The location of the docking interface is determined largely by geometric complementarity,
but finding complementary geometry is complicated by the flexibility of the backbone and side-chains of both proteins. We
seek to generate candidates for docking that approximate the bound state well, even in cases where there is backbone and/or
side-chain difference from unbound to bound states. |
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Keywords: | |
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