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Dynamic programming for sequence
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MODELLER A Program for
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MODELLER programming interface (API)
Contents
Index
Methods
Subsections
Dynamic programming for sequence and structure comparison and searching
Pairwise comparison
Variable gap penalty
Local
versus
global alignment
Similarity
versus
distance scores
Multiple comparisons
Optimization of the objective function by M
ODELLER
Function
Optimizers
Molecular dynamics
Langevin dynamics
Self-guided MD and LD
Rigid bodies
Rigid molecular dynamics
Rigid minimization
Equations used in the derivation of the molecular pdf
Features and their derivatives
Distance
Angle
Dihedral angle
Atomic solvent accessibility
Atomic density
Atomic coordinates
Restraints and their derivatives
Single Gaussian restraint
Multiple Gaussian restraint
Multiple binormal restraint
Lower bound
Upper bound
Cosine restraint
Coulomb restraint
Lennard-Jones restraint
Spline restraint
Symmetry restraint
Flowchart of comparative modeling by M
ODELLER
Loop modeling method
Ben Webb 2008-02-01
