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Protein Structure Prediction


Predicting low energy conformations for chemical compounds, peptides, nucleic acids etc.: Take a peptide sequence and predict its three-dimensional structure. Of course, the success is not guaranteed, especially if the peptide is longer than about 25 residues but some preliminary tests are encouraging. Evaluate local secondary structure preferences directly from the simulation. Watch a movie with your peptide folding.

Protein Modeling: ICM-Pro has a good record in protein modeling. There are procedures which will regularize or build the backbone, shake up the side-chains and loops by global energy optimization. You can also color the model by local reliability to identify the potentially wrong parts of the model. This does not include, however, the fast routine for building a complete model by homology with loops combined with the database search ( ICM-Homology is a separate add-on to ICM-Pro).

Loop modeling and protein design: ICM-Pro was used to design two new 7 residue loops and in both cases the designs were successful. Moreover, the predicted conformations turned out to be exactly right (accuracy of 0.5A) after the crystallographic structures of the designed proteins were determined by Rik Wierenga and his coworkers.

Key structure prediction features

Energy and Penalty Terms
A variety of energy and grid terms are available which are described in detail here
Set tethers restraints between atoms.
Delete tethers.
Set upper and lower boundaries of tethers.
Set tether weights.
Set tethers as a constant force.
Set distance restraints between atoms.
Minimization
Minimize Cartesian in Merck Molecular Force Field (MMFF)
Local minimization.
Minimize all atoms.
Minimize side chains.
Minimize hydrogens.
Minimize molecule position.
Adjust length of minimization.
Adjust a number of minimization parameters described here
Biased Probability Monte Carlo
Global optimization using the ICM Biased Probability Monte Carlo (BPMC) method (Abagyan et al 1994).
Adjust a number of BPMC parameters described here
Generate multiple receptor conformations (can be used in docking).
Optimize side chains.
Optimize ligand vicinity.
Optimize hydrogen bonds.
Loop Modeling
Sample loop conformations using BPMC
Fully-interactive table of loop conformations ranked by energy is displayed.
Click on the table to load loop conformation.
Force Fields
Select from 4 different force fields, ecepp, ecepp05, icmff and mmff
Set force field types and charges.
Regularization
Regularization options and features are described here
Edit Structure
Set bond type.
Set formal charge.
Set chirality.
Build hydrogens.
Set disulfide bonds.
Make bonds.
Make bonds by distance.
Delete bonds.
Set occupancy.
Set B-factor.
Make mutations and see the effect on energy of the structure or use for docking.
Modify group.
Randomize atoms.
Collection of Molecule Conformations(Stack).
View stack by loading a fully interactive clickable table.
Play all stack conformations in a loop (movie-like).
Add an additional conformation to an existing stack.
Store stack in an object.
Delete stack.
Compare conformations in a stack.
Recaluclate energies in a stack.
Impose a conformation from a stack onto an object.
Generate stack of normal mode backbone movements.

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