Boitechnology

The template is the first PDB hit found by using maximum four PSI-BLAST iterations in the NCBI nr data bank.

ESyPred3D is a automated Homology modeling program. The method gets benefit of the increased alignment performances of an alignment strategy that uses neural networks. Alignments are obtained by combining, weighting and screening the results of several multiple alignment programs. The final three dimensional structure is built using the modeling package MODELLER.

The usual four steps of homology modeling are executed: (1) search for a template (similar sequence of known structure), (2) align query and template sequences, (3) build the 3D model using the last alignment and the structure of the template and (4) assess the final 3D model.

ESyPred3D is a automated Homology modeling program. The method gets benefit of the increased alignment performances of an alignment strategy that uses neural networks. Alignments are obtained by combining, weighting and screening the results of several multiple alignment programs. The final three dimensional structure is built using the modeling package MODELLER.

eMovie is a plug-in for PyMOL that makes the creation of molecular movies both easy and intuitive via a breakthrough storyboard interface, similar in nature to what is used in the creation of traditional movies. [1]

eMovie is arguably the most user-friendly way for users to create movies in PyMOL (even inexperienced users). Users interact with a user-friendly eMovie GUI that does not require typing commands into PyMOL.Modular actions such as zooms, rotations, fadings, and morphs (morphs require incentive PyMOL) can be inserted to any frame in the movie and the actions comprising the movie can be reviewed in list-format by viewing the eMovie storyboard. The storyboard also allows for deletion and reinsertion of actions. Movies can be saved, loaded, and exported as a series of image files to be later merged into a traditional movie format such as .mov using an external program like GraphicConverter.

eMovie was created at the Israel Structural Proteomics Center [2] (ISPC) at the Weizmann Institute of Science, and is freely available for download. [3]

In computational geometry, the cone algorithm identifies surface particles quickly and accurately for three-dimensional clusters composed of discrete particles. It is especially useful for computational surface science and computational nano science. The cone algorithm was first described in a publication about nanogold in 2005. More detailed explanations and source code are available online. [1]

The cone algorithm works well with clusters in condensed phases, including solid and liquid phases. It can handle the situations when one configuration includes multiple clusters or when wholes exist inside clusters. It can also be applied to a cluster iteratively to identify multiple sub-surface layers

This is the core of the CoNTub[1] program. Strip algebra was implemented[3], which allows two perfect carbon nanotubes to be joined, independently of their geometry, radius or chirality, with the simplest geometry possible, i.e. with the lowest number of non-hexagonal rings (a pentagon and a heptagon), also called defects or disclinations. There is always a possible connection between two tubes and strip algebra ensues that the solution is unique and depending only of the indices (i,j) of both tubes.

To generate a SWNT, it is only necessary to introduce the indices of the tube, its desired length (Angstrom), and the type of atom for termination of dangling bonds. ConTub displays the resulting nanotube, as well as its electronic band structure and density of states (DOS), following a tight binding model.[2]

MWNT - multiple tubes with the same axis and length - are created by providing the indices of the most inner tube (i,j), the desired length (l), the number of shells (N), and the approximate distance between shells or spacing (S) in Angstrom. The default value for spacing corresponds to the standard distance between layers in crystalline graphite (3.4 Å). ConTub automatically selects the indices of the remaining tubes, trying to adjust the interlayer spacing, and tries to use tubes with the same chirality as that of the inner nanotube.

3D molecular viewer
Structure generation of carbon nanotube Heterojunctions from indices(i,j) and length (l) of the two nanotubes.
Structure generation of single-walled nanotubes (SWNTs) from indices(i,j) and length (l)
Plotting the electronic band structure and density of states (DOS) for single-walled nanotubes (SWNTs)
Structure generation of multi-walled nanotubes from indices(i,j) and length (l), number of shells(N) and spacing(S).
Output the xyz coordinates of the structures in a (PDB) file format

CoNTub is software written in Java which runs on Windows, Mac OS X, Linux and Unix Operating systems. It is the first implementation of an algorithm for generating the 3D structure of two arbitrary connected carbon nanotubes by means of one defect or disclination (pentagonal or heptagonal).

The software is a set of tools dedicated to the construction of complex carbon nanotube structures for use in computational chemistry. CoNTub[1] is the first implementation of building these complex structures, including nanotube heterojunctions, for designing and investigating new nanotube-based devices. CoNTub is based on strip algebra, and is able to find the unique structure for connecting two specific and arbitrary carbon nanotubes.

CoNTub[1] allows the geometry of some two-tube heterojunctions to be easily generated, including single-walled nanotubes (SWNTs) and multi-walled nanotubes (MWNTs). The program itself is organized in five Tabbed panelsCoNTub[1], the first three being dedicated to structure generation, the fourth to the output in PDB format, and the fifth contains a short help section.