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**Contents :**
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**//Note//**: All the data present in this database are derived from theoretical and computational calculations or obtained from experimental sources.
 

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====== Allotropy ======

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Allotropy is the property of some chemical elements to exist in two or more different forms, known as allotropes of these elements. Allotropes of the same element can exhibit quite different physical properties and chemical behaviours.
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Allotropes of carbon include diamond (where the carbon atoms are bonded together in a tetrahedral lattice arrangement), graphite (where the carbon atoms are bonded together in sheets of a hexagonal lattice), graphene (single sheets of graphite), and fullerenes (where the carbon atoms are bonded together in spherical, tubular, or ellipsoidal formations).
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In this package the structure of some allotropes are presented, such as graphite, graphene, diamond,etc.
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//**Screenshots**//

{{gallery>software::vmdmagazine::allotropy?*&250x250&lightbox}}

//**Version:**// (2013/10/03) {{:software:vmdmagazine:download:allotropy.zip| Version 1.1}}

//**Languages: **// en, pt


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====== Alkaloids ======
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Alkaloids are a group of naturally occurring chemical compounds that contain mostly basic nitrogen atoms. In addition to carbon, hydrogen and nitrogen, alkaloids may also contain oxygen, sulfur and more rarely other elements such as chlorine, bromine, and phosphorus.
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Alkaloids are produced by a large variety of organisms, including bacteria, fungi, plants, and animals, and are part of the group of natural products. Examples are the local anesthetic and stimulant cocaine; the psychedelic psilocin; the stimulant caffeine; nicotine; the analgesic morphine; the antibacterial berberine; the anticancer compoundvincristine; the antihypertension agent reserpine; the cholinomimeric galatamine; the spasmolysis agent atropine; the vasodilator vincamine; the anti-arhythmia compound quinidine; the anti-asthma therapeutic ephedrine; and the antimalarial drug quinine.
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In this package the structure of some alkaloids are presented, such as caffeine, cocaine.
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//**Screenshots**//
{{gallery>software:vmdmagazine:alkaloids?*&250x250&lightbox}}

//**Version:**// (2013/10/01) {{:software:vmdmagazine:download:alkaloids.zip| Version 1.1}}

//**Languages: **// en, pt
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====== Enzymes ======
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Enzymes are proteins that catalyse chemical reactions. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates sufficient for life. Since enzymes are selective for their substrates and speed up only a few reactions from among many possibilities, the set of enzymes made in a cell determines which metabolic pathways occur in that cell.
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Enzymes are in general globular proteins and range from just 62 amino acid residues in size to over 2,500 residues. The activities of enzymes are determined by their three-dimensional structure. However, although structure does determine function, predicting a novel enzyme's activity just from its structure is a very difficult problem that has not yet been solved.
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Like all catalysts, enzymes work by lowering the activation energy for a reaction, thus dramatically increasing the rate of the reaction. As a result, products are formed faster and reactions reach their equilibrium state more rapidly. Most enzyme reaction rates are millions of times faster than those of comparable un-catalyzed reactions. As with all catalysts, enzymes are not consumed by the reactions they catalyse, nor do they alter the equilibrium of these reactions.
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In this package are illustrated several biological systems that play key roles in  every biological system.
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//**Screenshots**//

{{gallery>software:vmdmagazine:enzymes?*&250x250&lightbox}}

//**Version:**// (2013/10/01) {{:software:vmdmagazine:download:enzymes.zip| Version 1.1}}

//**Languages: **// en, pt
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====== Intermolecular Forces ======
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Intermolecular forces are forces of attraction or repulsion which act between neighbouring particles: atoms, molecules or ions. They are weak compared to the intramolecular forces, the forces which keep a molecule together.
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Intermolecular forces become significant at molecular separations of about 1 nanometer or less, but are much weaker than the forces associated with chemical bonding. They are important, however, because they are responsible for many of the physical properties of solids, liquids, and gases. These forces are also largely responsible for the three-dimensional arrangements of biological molecules and polymers.
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In this package are illustrated several biological systems where the intermolecular interactions play an important role, such as hydrogen bonds, ionic bonds and “Pi” interactions.
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//**Screenshots**//

{{gallery>software:vmdmagazine:intforces?*&250x250&lightbox}}

//**Version:**// (2013/10/01) {{:software:vmdmagazine:download:chemical_bonds.zip| Version 1.1}}

//**Languages: **// en, pt
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====== Active Site Tunnels ======
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The active site of enzymes are generally protected from the solvent and found several angstroms away from the protein surface. 
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In this package are illustrated the tunnels that give access to several enzymes.
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//**Screenshots**//

{{gallery>software:vmdmagazine:active_site_tunnel?*&250x250&lightbox}}

//**Version:**// (2013/10/01) {{:software:vmdmagazine:download:active_site_tunnel.zip| Version 1.1}}

//**Languages: **// en, pt
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====== pH indicators Molecules ======
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A pH indicator is a halochromic chemical compound added in small amounts to a solution so the pH (acidity or basicity) of the solution can be determined visually  
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In this package are illustrated some molecules that behave as pH indicators.
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//**Screenshots**//

{{gallery>:software:vmdmagazine:phindicator?*&150x150&lightbox}}

//**Version:**// (2017/04/2) {{::software:vmdmagazine:download:ph_indicators.zip| Version 1.1}}

//**Languages: **// en
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====== Dyes ======
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A dye is a colored substance that has an affinity to the substrate to which it is being applied.
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In this package are illustrated some molecules that behave as dyes.
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//**Screenshots**//
{{gallery>:software:vmdmagazine:dyes?*&150x150&lightbox}}


//**Version:**// (2017/06/20) {{::software:vmdmagazine:download:dyes.zip|Version 1.1}}

//**Languages: **// en
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====== Protein Structure ======
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Protein structure is the three-dimensional arrangement of atoms in a protein molecule. Proteins are polymers formed from sequences of amino acids, the monomers of the polymer.
The term structure when used in relation to proteins, takes on a much more complex meaning than it does for small molecules. Proteins are macromolecules and have four different levels of structure – primary, secondary, tertiary and quaternary.

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In this package are illustrated some examples of the specific structures of proteins.

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//**Screenshots**//
{{gallery>:software:vmdmagazine:proteinstructure?*&150x150&lightbox}}

//**Version:**// (2016/12/20) {{::software:vmdmagazine:download:protein_structure.zip|Version 1.1}}

//**Languages: **// en
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====== Pharmaceutical Drugs ======
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A pharmaceutical drug (also referred to as medicine, medication, or simply as drug) is a drug used to diagnose, cure, treat, or prevent disease.

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In this package are illustrated some examples of molecules that are commercially available and are used clinically to create diseases.

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//**Screenshots**//
{{gallery>:software:vmdmagazine:pdrugs?*&150x150&lightbox}}


//**Version:**// (2017/03/2) {{::software:vmdmagazine:download:drugs.zip|Version 1.1}}

//**Languages: **// en
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====== Transition States ======
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The transition state of a chemical reaction is a particular configuration along the reaction coordinate. It is defined as the state corresponding to the highest potential energy along this reaction coordinate.

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In this package are illustrated some examples of transition states that were obtained from computational means.

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//**Screenshots**//
{{gallery>:software:vmdmagazine:ts?*&150x150&lightbox}}


//**Version:**// (2017/03/2) {{::software:vmdmagazine:download:transition_states.zip|Version 1.1}}

//**Languages: **// en
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