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Molecular dynamics (MD) simulations contain considerable information with regard to the motions and fluctuations of a protein, the magnitude of which can be used to estimate conformational entropy. Here we survey conformational entropy acros
Molecular dynamics (MD) simulations contain considerable information with regard to the motions and fluctuations of a protein, the magnitude of which can be used to estimate conformational entropy. Here we survey conformational entropy acros
Externí odkaz:
http://hdl.handle.net/10454/13021
Akademický článek
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Autor:
Towse, Clare-Louise, Daggett, V.
This chapter gives an introduction to protein simulation methodology aimed at experimentalists and graduate students new to in silico investigations. More emphasis is placed on the knowledge needed to select appropriate simulation protocols, leaving
Externí odkaz:
http://hdl.handle.net/10454/11549
Akademický článek
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The conformational propensities of amino acids are an amalgamation of sequence effects, environmental effects and underlying intrinsic behavior. Many have attempted to investigate neighboring residue effects to aid in our understanding of protein fol
Externí odkaz:
http://hdl.handle.net/10454/11432
Various host-guest peptide series are used by experimentalists as reference conformational states. One such use is as a baseline for random-coil NMR chemical shifts. Comparison to this random-coil baseline, through secondary chemical shifts, is used
Externí odkaz:
http://hdl.handle.net/10454/11545
Most rotamer libraries are generated from subsets of the PDB and do not fully represent the conformational scope of protein side chains. Previous attempts to rectify this sparse coverage of conformational space have involved application of weighting
Externí odkaz:
http://hdl.handle.net/10454/11546
D-amino acids are useful building blocks for de novo peptide design and they play a role in aging-related diseases associated with gradual protein racemization. For amino acids with achiral side chains, one should be able to presume that the conforma
Externí odkaz:
http://hdl.handle.net/10454/11547
Autor:
Towse, Clare-Louise, Daggett, V.
Membership in a protein domain database does not a domain make; a feature we realized when generating a consensus view of protein fold space with our consensus domain dictionary (CDD). This dictionary was used to select representative structures for
Externí odkaz:
http://hdl.handle.net/10454/11548