Method for Sampling Alpha-Helical Protein Backbones Page: 2 of 28
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at least 40% cite someone... of proteins of interest bear no discernible sequence resemblance
to a known macromolecule. Therefore ab initio prediction of structure from sequence remains
an important challenge.
When sequence homology cannot be used to construct a 3-D model, the current modus
operandi for predicting structure is composed of three separate (yet interdependent) steps:
sampling, searching, and ranking. One first picks a formalism to index and sample the
possible shapes, then searches through the shapes, and finally uses some ranking criterion to
pick out a structure as close to native as possible. To clarify this classification let us provide
some examples of each step.
sprinkle some citations here. very delicate situation, since we basically can site the whole
field in the next three paragraphs.
The first requirement in sampling structures is that of representation, e.g. all-atom,
reduced 'pseudo' amino-acid interaction centers, lattice, etc. Once the representation is
chosen, one then picks the degrees of freedom to use. Researchers vary Cartesian coordinates
of all or a subset of the atoms, dihedral angles, relative distances, and so on. The decisions
of which, how many, discretized or continuous, and so on, are motivated by the amount
of detail one wants to capture, as well as by computational complexity of the forthcoming
search. One notable example, similar in spirit to this work, is ref. [6] in which the authors
assemble helical sub-units using consensus distance geometry.
Having picked a representation, one then selects an appropriate search technique, or a
mixture of search techniques to march through the enormous space of possible 3-dimensional
structures. As we've mentioned above, the three complementary steps of prediction are
highly interdependent. The most important factors in picking a search method are compu-
tational complexity and the nature of the energy function and of the representation. Lattice
models, for instance, lend themselves easily to exhaustive enumeration. All atom cartesian
coordinate representations usually employ a physical potential, and search for a minimum
with either an intelligent minimization routine, or a copy of Nature's algorithm, molecular2
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Fain, Boris & Levitt, Michael. Method for Sampling Alpha-Helical Protein Backbones, article, February 22, 2000; Stanford, California. (https://digital.library.unt.edu/ark:/67531/metadc722208/m1/2/: accessed April 15, 2024), University of North Texas Libraries, UNT Digital Library, https://digital.library.unt.edu; crediting UNT Libraries Government Documents Department.