TOOLS:
HyperChem has included many modules to perform specific tasks molecular modeling functions.
Database Package
A full database capability is integrated into HyperChem 8. This includes database search and retrieval of molecules for subsequent molecular modeling calculations as well as the storing of computed properties and optimized structures of your molecules in a new database. Included with the product is a sample database of 10,000 molecules that have previously been optimized with HyperChem. The sample database that is included is representative of common chemical compounds and can be used in a variety of ways associated with research in computational chemistry.
NMR Simulation
The HyperNMR package has been integrated into the core of HyperChem. This package allows for the simulation of NMR spectra. An accurate semi-empirical tailored specifically to NMR allows rapid interactive computation of NMR shielding constants (chemical shifts) and coupling constants for molecules as large as proteins. Based on a solution of the quantum mechanical coupled-Hartree-Fock equations rather than simple database lookup, this package allows full exploration of NMR parameters in any situation, such as a new or novel chemical environment where simple database interpolation is impossible.
When appropriate, the NMR parameters can be integrated into a spin Hamiltonian to predict and display the full one-dimensional NMR spectra. The spectra can be manipulated to add line widths so as to simulate experimental spectra.
Web Viewer
The HyperChem Web Viewer is a free web browser plug-in that allows dynamic 3D views of molecules. Features include real-time rotation and manipulation, animation of normal modes, picking of spectral peaks and more. The Web Viewer can be used to view the results from HyperChem Professional Release 7.5, HyperChem 7 and HyperChem 6 or any of the molecules in the Hypercube online gallery. The Web Viewer provides an interactive 3D visual experience as opposed to the usual static picture.
Manipulate Protein Structures
Extensive additions have been made to HyperChem's ability to deal with protein structures. HyperChem now supports four secondary structure descriptions - helices, sheets, turns, and coils. The secondary structures can be individual selected, colored, and rendered using a new secondary structure rendering capability.
Docking by Optimization
"Docking" a small molecule onto a site on a larger molecule is a common task in biochemical investigations. HyperChem's extensive structure optimizing capabilities provide an effective route for exploring the structure of docked systems.
Given the two molecules, and a hypothesis as to which pairs of atoms are adjacent, the docking calculation can be started by constructing a set of optimizer restraints specifying those distances. Once these restraints are in place, select the small molecule, and optimize its structure. The restraint forces pull it into place in the docking site. Once complete, the restraints can be removed and a final optimization completed to get an accurate structure.
RMS Fit
RMS Fit provides a new tool for comparing structures of molecules in HyperChem, augmenting the existing overlay function and the flexible fitting provided by restrained optimizations. The RMS Fit module lets you carry out the following tasks:
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Overlay two molecules by minimizing the distance between corresponding atoms in the two target molecules, displaying the residual error.
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Have the corresponding atoms be all atoms, or selected atoms only.
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Designate the corresponding atoms by their numbering within a molecule, or by the order in which you select them.
Sequence Editor
Sequence Editor provides additional tools for manipulating strings of amino acids in HyperChem. The Sequence Editor brings the following capabilities to HyperChem:
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Read FASTA files consisting of strings of one-letter amino acid designators.
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Specify secondary structure, including alpha helix, extended, parallel and anti-parallel beta sheets, three types of beta turns, and random coil, and put the resulting structure into HyperChem.
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Get polypeptides from HyperChem with secondary structure designators.
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Search for specific amino acid sequences in a polypeptide.
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Show the polarity of each amino acid in the sequence, and display the distribution of each type.
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Compare the similarity of two polypeptides, using a Dayhoff matrix (dot plot) approach.
Crystal Builder
With Crystal Builder you can build up crystals in HyperChem by hand, by entering fractional coordinates, or choose from a set of samples provided. Crystal Builder gives you control over the face you view, and the size of the crystal you build; it also allows you to read Cambridge Crystal Database files into HyperChem. The Crystal Builder includes the following features:
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Read in Cambridge Crystallographic Database files (FDAT), and place them in HyperChem.
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Over 20 sample crystal structures included, particularly useful in educational contexts.
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Control crystal size and shape (number of unit cells in each direction).
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Control which crystal face you view, by specifying Miller indices.
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For manual building of crystals, you can specify unit cell angles and lengths (a, b, c) for each of the eight basic crystal types, plus face centered cubic and body-centered cubic. All distinct space groups are not included, so you may need to calculate special positions as required for the different space groups.
Sugar Builder
With Sugar Builder you can construct polysaccharides from individual saccharide components. The Sugar Builder's features include the following:
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Build polysaccharides from aldoses and ketoses, as well as amino sugars and N-acyl sugars, Inositol and deoxy sugars.
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Terminate the polysaccharides using any of the thirteen blocking groups provided.
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For each saccharide, you have control over the isomer (D or L), the form (acyclic, a, or b), the angles (f, y and w), and the connection site.
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Construct polymers from other, possibly non-saccharide, components using the user-defined component dialog box.
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Link polysaccharide strands, with full specification of site and angles.
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Carry out simulations, using an extension of the AMBER force field specifically intended for saccharides [S. W. Homans, Biochemistry 29, 9110 (1990)]. This force field allows you to carry out calculations on some, but not all, polysaccharides. (HyperChem's MM+ force field will also compute properties of polysaccharides).
Conformational Search
The Conformational Search module is a tool for finding and saving stable structures of molecules, using stochastic approaches based on modification of torsion angles.
Conformational Search has a wide range of options to tune the search for your particular needs. The general approach is to twist selected torsion angles of the system to distort a structure and, if certain tests are met, optimize to obtain a new candidate structure. The new structure can be accepted or rejected as a structure of interest according to a variety of criteria. Here is a list of some of the more important facilities of Conformational Search:
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Select the torsion angles you wish to vary using HyperChem's selection methods.
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Study ring flexibility using our implementation of the torsional flexing method of Kolossvary and Guida [J. Comput. Chem., 14, 691, (1993)].
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Choose between random walk and a usage-directed approach [G. Chang, W. C. Guida and W. C. Still, J. Am. Chem. Soc., 111, 4379 (1989)] to generate a sequence of conformations.
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Save all acceptable structures as the run progresses, and restart previous searches.
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Filter structures prior to optimization by checking for close contacts and torsion angles that are similar to previously optimized structures, and after optimization for inversion of chiral centers.
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Following optimization, eliminate duplicate structures by comparing energies, torsion angles, and RMS fit residual errors, automatically taking account of user specified equivalent atoms.
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Save full details of the search to a file. Structures can be read back in and put into HyperChem by simply selecting the structure of interest and executing a single command.
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Display results in tables that can be copied into spreadsheets for further analysis.
Script Commands
A script command is a text instruction that tells HyperChem to carry out a task or requests information from HyperChem. A script is a text file containing a list of script commands, which are sent in sequence to HyperChem. The HyperChem documentation contains a full listing and description of more than 400 script commands.
Once a script file has been created, you can execute it from the HyperChem user interface, using the Script menu. Up to ten custom commands, complete with keyboard shortcuts, can appear on the Script menu. You can then simply click on a menu item to execute the appropriate script. Scripts can be used in many ways to:
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Carry out batch calculations.
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Automate frequent tasks.
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Set the visualization and computation options appropriate for different tasks.
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Launch other programs from HyperChem.
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Have HyperChem automatically read a particular file (called chem.scr) on startup to initialize your settings and carry out any task you always want executed upon start-up.
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Ensure that a set of calculations is carried out with exactly the same settings in every case.
HyperChem and Spreadsheets
You can write a macro in a Windows spreadsheet program that supports DDE (for example, Microsoft Excel) and bring spreadsheet capability to HyperChem. A macro can be used to:
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Automatically carry out a set of calculations on a set of molecules and read the results into the spreadsheet for analysis and convenient organization of results.
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Automatically carry out systematic searching of dihedral angles for stable conformations.
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Carry out dynamics calculations and read the results into a spreadsheet for analysis.
Read an Overview of HyperChem's features.
Read about HyperChem's Computational Methods.
Read about HyperChem's stunning visualizations.
Read about HyperChem's other tools for molecular modeling.
Purchase HyperChem 8 Professional.
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