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*  Distance geometry problem
Crippen and Havel are two pioneers of DGP, and they co-authored the book "Distance Geometry and Molecular Conformation", 1988. ... Crippen, G.M.; Havel, T.F. (1988). "Distance Geometry and Molecular Conformation". John Wiley & Sons. Biswas, P.; Lian, T.; ... When dealing with biological molecules, the DGP is generally referred to as molecular DGP (MDGP). In the following, even if the ... This is a package for molecular modeling and design. It includes many force fields for attempting the prediction of protein ...
*  Decamethonium
"Molecular conformation-activity relationship of decamethonium congeners". Br J Anaesth. 88 (5): 692-9. doi:10.1093/bja/88.5.692 ...
*  Dihedral angle
... s are used to specify the molecular conformation. Stereochemical arrangements corresponding to angles between 0° ... The synperiplanar conformation is also known as the syn- or cis-conformation; antiperiplanar as anti or trans; and synclinal ... The syn-conformation shown above, with a dihedral angle of 60° is less stable than the anti-configuration with a dihedral angle ... Application to side-chain prediction". Journal of Molecular Biology. 230 (2): 543-74. doi:10.1006/jmbi.1993.1170. PMID 8464064 ...
*  Neosaxitoxin
Sheets MF, Fozzard HA, Lipkind GM, Hanck DA (January 2010). "Sodium channel molecular conformations and antiarrhythmic drug ... Molecular toxicology. 1 (2-3): 209-16. PMID 3130568. Schwartz DM, Duncan KG, Fields HL, Jones MR (October 1998). "Tetrodotoxin ...
*  C3a receptor
Reid RC, Yau MK, Singh R, Lim J, Fairlie DP (August 2014). "Stereoelectronic effects dictate molecular conformation and ... Molecular Immunology. 35 (3): 137-48. doi:10.1016/S0161-5890(98)00021-2. PMID 9694514. Lienenklaus S, Ames RS, Tornetta MA, ... "Molecular cloning and characterization of the human anaphylatoxin C3a receptor". The Journal of Biological Chemistry. 271 (34 ...
*  Calponin 1
Jin JP, Walsh MP, Sutherland C, Chen W (September 2000). "A role for serine-175 in modulating the molecular conformation of ... Ser175 phosphorylation alters the molecular conformation of calponin and dissociates calponin from F-actin. The consequence is ... Masuda H, Tanaka K, Takagi M, Ohgami K, Sakamaki T, Shibata N, Takahashi K (August 1996). "Molecular cloning and ... Burgstaller G, Kranewitter WJ, Gimona M (May 2002). "The molecular basis for the autoregulation of calponin by isoform-specific ...
*  CHELPG
It should be remembered that atomic charges depend on the molecular conformation. The representative atomic charges for ... While CHELPG is restricted to non-periodic (e.g., molecular) systems, the DDEC methods can be applied to both non-periodic and ... flexible molecules hence should be computed as average values over several molecular conformations. A number of alternative ... The charge calculation methods based on fitting of molecular electrostatic potential (MESP) (including CHELPG) are not well- ...
*  1,5-Cyclooctadiene
The molecular conformation of (E,E)-COD is twisted rather than chair-like. The compound has been investigated as a click ... Boeckh, Dieter; Huisgen, Rolf; Noeth, Heinrich (1987). "Preparation and conformation of (E,E)-1,5-cyclooctadiene". J. Am. Chem ...
*  Arieh Warshel
Crystal Structure, Sublimation Energies, Molecular and Lattice Vibrations, Molecular Conformations and Enthalpies of Alkanes". ... the combined Quantum Chemistry/Molecular mechanics (i.e., QM/MM) method for simulating enzymatic reactions, the first molecular ... Warshel A. (2002). "Molecular Dynamics Simulations of Biological Reactions". Acc. Chem. Res. 35 (6): 385-395. doi:10.1021/ ... Lifson S, Warshel A. (1968). "A Consistent Force Field for Calculation on Conformations, Vibrational Spectra and Enthalpies of ...
*  Protein purification
Affinity Chromatography is a separation technique based upon molecular conformation, which frequently utilizes application ... Second, proteins can be separated according to their size or molecular weight via size exclusion chromatography or by SDS-PAGE ... and it is not able to distinguish between proteins with similar apparent molecular weight. If the protein has a distinguishing ... milder detergents such as Triton X-100 or CHAPS can be used to retain the protein's native conformation during complete ...
*  Strain (chemistry)
A highly strained, higher energy molecular conformation will spontaneously convert to the lower energy molecular conformation. ... The equilibrium of two molecular conformations is determined by the difference in Gibbs free energy of the two conformations. ... The anti conformation of butane is approximately 0.9 kcal mol−1 (3.8 kJ mol−1) more stable than the gauche conformation. Both ... For example, n-butane has two possible conformations, anti and gauche. The anti conformation is more stable by 0.9 kcal mol−1. ...
*  Merlin (protein)
Ali Khajeh, J; Ju, JH; Atchiba, M (2014). "Molecular conformation of the full-length tumor suppressor NF2/Merlin--a small-angle ... conformation and suppresses cell growth and motility". Hum. Mol. Genet. 10 (8): 825-34. doi:10.1093/hmg/10.8.825. PMID 11285248 ... neutron scattering study". Journal of Molecular Biology. 426 (15): 2755-68. doi:10.1016/j.jmb.2014.05.011. PMC 4407695 . PMID ...
*  Isolobal principle
For example, the possibility of unsynthesized compounds can be imagined from those of known molecular conformations. The ... the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO). Isolobal compounds are ... Roald Hoffmann described molecular fragments as isolobal "if the number, symmetry properties, approximate energy and shape of ... The molecule retains its molecular geometry as the frontier orbital points in the direction of the missing hydrogen atom. ...
*  Global optimization
... transformation scheme as a special continuation approach to global optimization with application to molecular conformation. ... Phys., 7, 3910 Y. Sugita and Y. Okamoto (1999). "Replica-exchange molecular dynamics method for protein folding". Chemical ... this is usually known as replica-exchange molecular dynamics or REMD. Essentially, one runs N copies of the system, randomly ... problems The starting point of several molecular dynamics simulations consists of an initial optimization of the energy of the ...
*  Equilibrium unfolding
As usual in statistical mechanics, these states correspond to ensembles of molecular conformations, not just one conformation. ... 1992) "Physical Basis for the Stability of the Folded Conformations of Proteins", in Protein Folding, TE Creighton, ed., W. H. ... which reports the molecular size and fold density) and near-ultraviolet fluorescence (which reports on changes in the ...
*  Symmetry number
In statistical thermodynamics, the symmetry number corrects for any overcounting of equivalent molecular conformations in the ... operations Point groups in three dimensions Space group in 3 dimensions Symmetry combinations in 2 dimensions Molecular ...
*  Tinker (software)
"Algorithms for calculating excluded volume and its derivatives as a function of molecular conformation and their use in energy ... molecular modeling Comparison of software for molecular mechanics modeling Molecular dynamics Molecular geometry Molecular ... application for molecular dynamics simulation with a complete and general package for molecular mechanics and molecular ... Ponder, Jay W.; Richards, Frederic M. (1987). "An efficient newton-like method for molecular mechanics energy minimization of ...
*  GroEL
The constricted nature of the interior of the molecular complex strongly favors compact molecular conformations of the ... The addition of ATP and GroES has a drastic effect on the conformation of the cis domain. This effect is caused by flexion and ... GroEL belongs to the chaperonin family of molecular chaperones, and is found in a large number of bacteria. It is required for ... Vélez-Granell CS, Arias AE, Torres-Ruíz JA, Bendayan M (1994). "Molecular chaperones in pancreatic tissue: the presence of ...
*  Herbert S. Gutowsky
... its relation to molecular structure has provided the chemist with working tools to study molecular conformation and molecular ... 3) Gutowsky discovered spin-spin coupling in molecular liquids and understood its implications for the study of molecular ... establishing that energy barriers existed between molecular conformations. They were able to demonstrate that molecules "jumped ... However, it was difficult to find molecular systems whose exchange rate could be monitored precisely enough to observe this. ...
*  Distributed multipole analysis
... the DMA captures features of the molecular charge distribution that depend strongly on molecular conformation. Thus, in a DMA- ... If the molecular orbitals are written as linear combinations of atomic basis functions the electron density takes the form of a ... It may therefore seem surprising that it has not been more widely used in molecular simulation. Possible reasons for this are: ... Rein, R. (1973). "On Physical Properties and Interactions of Polyatomic Molecules: With Application to Molecular Recognition in ...
*  Branching (polymer chemistry)
Branched polymers have more compact and symmetrical molecular conformations, and exhibit intra-heterogeneous dynamical behavior ... Also, Ziegler-Natta monomers have to be small, and it was still impossible to control the molecular mass of the polymer chains ... Alexandros Chremos; E. Glynos; P. F. Green (2015). "Structure and dynamical intra-molecular heterogeneity of star polymer melts ...
*  Nanomotor
DNA nanomachines, based on changes between two molecular conformations of DNA in response to various external triggers, have ... A proposed branch of research is the integration of molecular motor proteins found in living cells into molecular motors ... A nanomotor is a molecular or nanoscale device capable of converting energy into movement. It can typically generate forces on ... Starting and stopping the movement of such motor proteins would involve caging the ATP in molecular structures sensitive to UV ...
*  Quantitative structure-activity relationship
... some conformation of the molecule). On June 18, 2011 the Comparative Molecular Field Analysis (CoMFA) patent has dropped any ... each of which represents a possible molecular conformation. A label or response is assigned to each set corresponding to the ... Conformation-activity relationship Differential solubility Molecular design software Partition coefficient Pharmacokinetics ... "Prediction-driven matched molecular pairs to interpret QSARs and aid the molecular optimization process". Journal of ...
*  TNNI3
Akhter S, Zhang Z, Jin JP (Feb 2012). "The heart-specific NH2-terminal extension regulates the molecular conformation and ... Vallins WJ, Brand NJ, Dabhade N, Butler-Browne G, Yacoub MH, Barton PJ (Sep 1990). "Molecular cloning of human cardiac troponin ... extension contains the PKA phosphorylation sites Ser23/Ser24 and plays a role in modulating the overall molecular conformation ... Perry SV (Jan 1999). "Troponin I: inhibitor or facilitator". Molecular and Cellular Biochemistry. 190 (1-2): 9-32. doi:10.1023/ ...
*  Crystallography
X-ray crystallography is the primary method for determining the molecular conformations of biological macromolecules, ... In spite of this, a certain amount of molecular information can be deduced from patterns that are generated by fibers and ... Computer programs such as RasMol or Pymol can be used to visualize biological molecular structures. Neutron crystallography is ...
*  Sequence motif
Biology portal Molecular and cellular biology portal Biomolecular structure MaMF (Mammalian Motif Finder), an algorithm for ... "An approach to detection of protein structural motifs using an encoding scheme of backbone conformations" (PDF). Proc. of 2nd ...