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• Smile Format
  ... e 1980s.This format used the concept of graph in which nodes represent the atoms and edge
  627 B (92 words) - 04:00, 31 July 2008
• Molecular Mechanics
  ... al method of calculating the dynamics of molecules, in which bonds between atoms are represented by springs obeying Hooke's law, and additional terms repre ... *Interactions must be preassigned to specific sets of atoms.
  8 KB (1146 words) - 08:33, 26 August 2008
• Homology Modeling
  ... ted steric conflicts arising from the van der Waals radii of the divergent atoms between target and template. ... dient energy minimization to iteratively refine the positions of all heavy atoms in the protein.
  9 KB (1291 words) - 11:19, 19 August 2008
• Chemical file format
  ... d-column-width format and thus officially has a built-in maximum number of atoms; however, many tools can read files that exceed the limit. Some PDB files ... ... is file is composed of several parts, separated by a tag (!Header, !Info, !Atoms, !Bonds, !Coord, !PartialCharges and !End).
  14 KB (2238 words) - 09:36, 17 September 2008
• Docking (molecular)
  ... ribe the hydrophobic features of the protein using turns in the main-chain atoms. Yet another approach is to use a Fourier shape descriptor technique. Wher ...
  12 KB (1708 words) - 05:48, 17 September 2008
• Protein structure
  <script>spin on;color atoms amino;</script> <script>color atoms amino</script>
  27 KB (4092 words) - 12:18, 4 December 2008
• Software for molecular mechanics modeling
  ... RMM for fast stable inaccurate optimization of single molecules up to 1000 atoms
  6 KB (829 words) - 07:46, 18 August 2008
• DNA
  82 KB (11827 words) - 06:08, 20 August 2008
• Protein Data Bank
  ... atom]]s in a large biomolecule (although, usually without the [[hydrogen]] atoms, as their positions are more of a statistical estimate); if one is only in ...
  11 KB (1705 words) - 05:34, 19 August 2008
• RNA
  ... ing.png|thumb|right|230px|Watson-Crick base pairs in a [[siRNA]] (hydrogen atoms are not shown)]]
  31 KB (4467 words) - 07:24, 20 August 2008
• Hydrogen bond
  ... ve partial charge. Because of the small size of hydrogen relative to other atoms and molecules, the resulting charge, though only partial, nevertheless rep ... ... e figure (two through its two lone pairs, and two through its two hydrogen atoms.)
  19 KB (2877 words) - 09:05, 20 August 2008
• BIAdb Berberine 1438
  ... ' border=1><tr><td><jmol><jmolApplet><size>200</size><script>spin on;color atoms amino;</script><uploadedFileContents>2353.SDF</uploadedFileContents><color ...
  2 KB (244 words) - 08:26, 10 December 2009
• Computational chemistry
  ... h properties are structure (i.e. the expected positions of the constituent atoms), absolute and [[interaction energy|relative]] (interaction) [[energy|ener ... ... because they employ experimental results, often from acceptable models of atoms or related molecules, to approximate some elements of the underlying theor ...
  29 KB (4051 words) - 07:26, 25 August 2008
• Molecul;ar Modelling
  ... hat it reduces the complexity of the system, allowing many more particles (atoms) to be considered during simulations. ... ]. The electrostatic interactions are computed based on [[Coulomb's law]]. Atoms are assigned coordinates in Cartesian space or in [[internal coordinates]] ...
  8 KB (1088 words) - 09:16, 1 September 2008
• Simulated annealing
  22 KB (3441 words) - 08:51, 26 August 2008
• Lattice protein
  3 KB (481 words) - 09:52, 17 September 2008
• Molecular graphics
  ... and [[Kekule]]'s [[benzene]], there has been a rich history of hand-drawn atoms and molecules, and these representations have had an important influence o ... ... s and planar sheets, but the most widely used approach is to represent all atoms and bonds explicitly using the "ball and stick" approach. This can demonst ...
  26 KB (3817 words) - 04:05, 27 August 2008
• DRUG INFORMATION SOURCES
  ... e chemical constitution of a drug. It indicates the precise arrangement of atoms and atomic groups in the molecule. However, chemical names are too complex ...
  14 KB (2095 words) - 05:21, 9 September 2008
• Natural product drug discovery
  ... re of heteroatoms (O and N enriched in natural products, and S and halogen atoms more often present in synthetic compounds), as well as level of non-aromat ... ... ural products. NMR yields information about individual hydrogen and carbon atoms in the structure, allowing detailed reconstruction of the molecule’s arc ...
  13 KB (1907 words) - 06:09, 17 September 2008
• Energy minimization
  ... one or two coordinates. For example, the vander Waals energy of two argon atoms depends upon just one coordinate: the interatomic distance. Sometimes one ... ... n minimum points on the energy surface. Minimum energy arrangements of the atoms correspond to stable states of the system; any movement away from a minimu ...
  3 KB (449 words) - 09:57, 1 September 2008

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