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- The clusters, hinges, and related dihedrals of
Met-enkephalin, shown in .
- Proteins and peptides used in NEIMO simulations. The structures listed
are the initial Protein Database files, except for the peptides
``MEnk'' and ``Ala9,'' which were created using the BIOGRAF peptide
- Timing results for the ten protein/peptides systems studied
here. The average times per timestep of the NEIMO calculation and the
nonbond calculation are given, along with the NEIMO time divided by
, and the nonbond time
divided by the number of atoms, .
- The average values of the Met-enkephalin dihedrals from 5 ps
NEIMO () and Cartesian () dynamics
simulations, compared to the initial values and compared to
- Crystal structures used in the H64 dataset.
- The number of samples of the three residue types in the protein
- This table lists the number of (and percentage of the maximum
possible) gridpoints which have
non-zero values for each of the three residue types at different grid
- This table lists the number of high-probability gridpoints: the
number which have probabilities above .
- This highest-probability gridpoint of each residue type for each grid
- The percentage of sample 's falling within each quadrant
of conformational space.
- The distribution of secondary structure designations in the
crystal structures of the SS58 dataset.
- The number of PGMC dihedrals () for each amino
acid, the number of occurrences of each amino in the H64 crystal
structures, and the number of populated (non-zero) gridpoints at each
grid spacing. for alanine and glycine. The numbers in
italics are more than 95%of the sample size, indicating that nearly
every conformation occupies a different gridpoint.
- The total number of gridpoints for dihedrals at
different grid spacings.
- The number of populated gridpoints in the , distribution
of amino acids with . Lysine appears to be the most flexible
while tryptophan is the least flexible.
- The highest-probability gridpoint for each amino acid for .
is the probability of this particular conformation.
- Conformations generated for Met-enkephalin from peak , ,
and gridpoints at different grid spacings. Because of steric
overlap, the energy of the 5 conformation is greater than
- Conformations generated from peak , , and
gridpoints at different grid spacings, after minimization with the DREIDING
forcefield. The energy of each conformation is given, along with the RMS
deviation from its original (un-minimized) structure.
- LS is the structure produced by rotating the dihedrals of our
starting structure to the values reported for the ECEPP/2 global minimum
. LS was obtained by a Cartesian-coordinate
conjugate-gradients minimization of LS using the DREIDING forcefield.
- Dihedral numbering used in and
- regions indicating residue is likely to be in an
helix or sheet conformation; i.e., its and fall within
the corresponding region listed in the lower table. and
are defined in .
- Variables used in PGMC C Builder. For Phase 1, ``steps''
refers to the number of conformations sampled as each residue is
added. For Phase 2, it refers to the total number of conformations sampled.
- Values used for production runs of the C Builder.
- The energy, rms deviation in backbone atoms (RMSB), and rms
deviation in dihedrals (RMSD) for each of the 20 backbone conformations
generated for crambin.
- The energy and rms deviation in atomic
coordinates for each of the crambin models produced by the PGMC C
- RMS deviations for different regions of the crambin model.
- The rms deviations in various types of dihedrals for the
crambin model and the percentage of each type of dihedral with
deviations less than 30 or more than 90.
- The proteins modeled by the PGMC C Builder. The
reference crystal structure is given along with the number of residues
in the protein and the percent of these which are in helices and sheets.
- The results from Phase 1 constructions of the backbone
conformations of several proteins.
- The results from Phase 2 constructions of the sidechains of
crambin, plastocyanin, and flavodoxin.
- A comparison of the results for flavodoxin vs. other
methods. ``Correct'' refers to dihedrals predicted to within 20 of their
crystal structure values.
- Equilibrium geometries and force constants in the CFF.
- Best-fit fcc lattice conformations of several proteins,
before and after minimization with the CFF.
- Results from building all-atom conformations from various
C conformations of crambin using the PGMC C Builder.
- The loop residues of HyHEL-5 and McPC603.
- The rms deviations for all atoms, backbone atom (BB), and C
coordinates are given for the predicted conformations of the McPC603
- The lowest-energy loops created in phases 1 and 2 of
simulations of HyHEL-5.
- The best rms deviation of C coordinates from the crystal
structure from among the 1000 loops generated in Phase 1.
- The results from this work (PGMC) compared to results from
three different methods: a conformational-search
algorithm, a method which uses the canonical
structures of loops other than H3 (L3 of HyHEL-5 also does not fit one
of the canonical structures), and a method which
combines conformational searching with comparisons to database