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Various molecular structures formed only by rotation about single bonds
In chemistry, rotamers are chemical species that differ from one another primarily due to rotations about one single bond. Various arrangements of atoms
Rotamer
Rational design of new protein molecules
conformations termed rotamers. Rotamer libraries are derived from the statistical analysis of many protein structures. Backbone-independent rotamer libraries describe
Protein_design
Topics referred to by the same term
Gauche effect, a characterization in which the gauche rotamer is more stable than the anti rotamer Gauche (Scheme implementation), an implementation of
Gauche
Collection of data on conformations of a given protein's amino acid side chains
backbone-dependent rotamer library provides the frequencies, mean dihedral angles, and standard deviations of the discrete conformations (known as rotamers) of the
Backbone-dependent rotamer library
Backbone-dependent_rotamer_library
Steric effect from the spatial arrangement of methyl groups in n-pentane
side chain rotamer frequencies and their mean dihedral angles, which is evident from statistical analysis of protein side-chain rotamers in the Backbone-dependent
Pentane_interference
Type of biological prediction
known as "rotamers". The methods attempt to identify the set of rotamers that minimize the model's overall energy. These methods use rotamer libraries
Protein_structure_prediction
Type of dihedral angle
direct steric interactions between the Cγ of the side chain in the gauche+ rotamer and the backbone nitrogen of the next residue when ψ is near −60°. This
Torsion_angle
Molecular-structural phenomenon
length is higher for the anti-rotamer (151.4 pm vs. 150 pm). The steric repulsion between the fluorine atoms in the gauche rotamer causes increased CCF bond
Gauche_effect
Angle between two planes in space
direct steric interactions between the Cγ of the side chain in the gauche+ rotamer and the backbone nitrogen of the next residue when ψ is near −60°. This
Dihedral_angle
val, thr, etc.) likely to have wrong rotamers. 2.0 - 2.5 As 2.5 - 3.0, but number of sidechains in wrong rotamer is considerably less. Many small errors
Resolution (structural biology)
Resolution_(structural_biology)
Probability distribution on a torus
model of protein structure in atomic detail, such as backbone-dependent rotamer libraries. The bivariate von Mises distribution is a probability distribution
Bivariate von Mises distribution
Bivariate_von_Mises_distribution
rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, and Ramachandran idealization. The software is designed to be easy-to-learn
Coot_(software)
Pairs of molecules with same chemical formula showing different spatial orientations
to the Study of the Gauche Effect. The Complete Structure of the Anti Rotamer of 1,2-Difluoroethane". J. Am. Chem. Soc. 119 (20): 4789. doi:10.1021/ja963819e
Cis–trans_isomerism
Symmetry of molecules of chemical compounds
(staggered rotamer) octafluoroxenate ion (idealized geometry) D5d E 2C5 2C52 5C2 i 2S103 2S10 5σd 36° twist ferrocene (staggered rotamer) Ruthenocene
Molecular_symmetry
Protein design algorithm
FoldX can mutate protein and DNA side chains using a probability-based rotamer library, while exploring alternative conformations of the surrounding side
FoldX
Computational chemistry software package
based on OpenBabel, which provides basis functionality like atom typing, rotamer generation and import/export of chemical file formats. Open Babel — chemical
Ghemical
When molecules have the same atoms and bond structure but differ in 3D orientation
24=16 possible stereoisomers. Descriptor (chemistry) Backbone-dependent rotamer library IUPAC, Compendium of Chemical Terminology, 5th ed. (the "Gold Book")
Stereoisomerism
Algorithm for minimizing a function over a set of independent variables
DEE description included criteria for the elimination of single rotamers and of rotamer pairs, although this can be expanded. In the following discussion
Dead-end_elimination
Entropy associated with a molecule's possible conformations
assigned an energy. In proteins, backbone dihedral angles and side chain rotamers are commonly used as parameters, and in RNA the base pairing pattern may
Conformational_entropy
Chemical compound
is a bent molecule with an O−C−O angle of 105.6° for the C2v all-trans rotamer. Although stable at 10 K, at higher temperatures it isomerizes to formic
Dihydroxymethylidene
isomeric conformers (which are not absolute) of either its anti- or gauche- rotamer. The variant with optimized efficacy is not the usually attested generic
List of methylphenidate analogues
List_of_methylphenidate_analogues
American biochemist and biophysicist (1925–2009)
solvent accessibility and internal packing of proteins, the first side-chain rotamer library, high-pressure crystallography, new types of chemical tags such
Frederic_M._Richards
Pharmaceutical compound
phase. The 4-phenylbutylamine molecule exists in the form of four stable rotamers. A serine protease inhibitor, it has been used in research as a test inhibitor
4-Phenylbutylamine
Stereoisomerism due to hindered rotation
barrier to rotation that is high enough to allow for isolation of individual rotamers. They occur naturally and are of occasional importance in pharmaceutical
Atropisomer
Drug discovery and development
intramolecular cyclization is the conversion of the trans-rotamer, which is the DPP-4 binding rotamer (Figure 5). Thus, preventing this conversion will increase
Discovery and development of dipeptidyl peptidase-4 inhibitors
Discovery_and_development_of_dipeptidyl_peptidase-4_inhibitors
Chemical compound
efficient and reactive catalysis during olefin metathesis. Two distinct rotamers—syn and anti—exist due to the orientation of the alkylidene ligand relative
Molybdenum imido alkylidene complex
Molybdenum_imido_alkylidene_complex
System of connected p-orbitals with delocalized electrons in a molecule
C. (2009-02-05). "High Level ab Initio Energies and Structures for the Rotamers of 1,3-Butadiene". The Journal of Physical Chemistry A. 113 (8): 1601–1607
Conjugated_system
Chemical group attached to backbone
computational tools for side-chain reconstruction. Alkyl Backbone-dependent rotamer library Backbone chain Branching (polymer chemistry) Functional group Pendant
Side_chain
each possible rotamer at each position, and the probability of a given structure is defined as a function of the probabilities of its rotamer components
Self-consistent mean field (biology)
Self-consistent_mean_field_(biology)
Type of saturated hydrocarbon compound
Ball-and-stick models of the two rotamers of ethane
Alkane
Chemical reaction
contain either a destabilizing syn-pentane interaction or an anti-Felkin rotamer, Z-enolates are less diastereoselective: If both the enolate and the aldehyde
Aldol_reaction
for other environments (e.g. excluded ligand volumes), loop modelling, rotamer libraries for sidechain conformations, relaxation using MM forcefields
List of protein structure prediction software
List_of_protein_structure_prediction_software
Technique used for determining crystal structures and identifying mineral compounds
structural validation suite ProSA-web NQ-Flipper (check for unfavorable rotamers of Asn and Gln residues) DALI server (identifies proteins similar to a
X-ray_crystallography
x_{b}^{j_{q}})} is the energy of interaction between rotamer state p of residue X i s {\displaystyle X_{i}^{s}} and rotamer state q of residue X j s {\displaystyle
Graphical models for protein structure
Graphical_models_for_protein_structure
Covalent bond between carbon and fluorine atoms
to the Study of the Gauche Effect. The Complete Structure of the Anti Rotamer of 1,2-Difluoroethane". J. Am. Chem. Soc. 119 (20): 4789–4790. doi:10.1021/ja963819e
Carbon–fluorine_bond
amino acids' side chains dihedral angles are often approximated from a rotamer library, but can worsen the inaccuracy of side chain packing in the overall
Loop_modeling
Antibiotic medication
Vancomycin exhibits atropisomerism—it has multiple chemically distinct rotamers owing to the rotational restriction of some of the bonds. The form present
Vancomycin
Chemical compound
exists as two rotamers that can be distinguished by NMR spectroscopy. The two principal resonance structures for one of these rotamers is shown: This
N-Methylformamide
Molecular modelling software
calculation of centroids, axes, planes and associated measurements amino acid rotamer libraries, protein Ramachandran plot, protein contact map structure building
UCSF_Chimera
Italian chemist
Yevhen Polyhach; Enrica Bordignon; Gunnar Jeschke (30 November 2010). "Rotamer libraries of spin labelled cysteines for protein studies". Physical Chemistry
Enrica_Bordignon
Pharmaceutical compound
it should not be assumed that "inactive" conformationally constrained rotamers are necessarily pharmacologically inactive; results depend on the similarity
DOM-CR
Chemical compound
February 2009). "High Level ab Initio Energies and Structures for the Rotamers of 1,3-Butadiene". The Journal of Physical Chemistry A. 113 (8): 1601–1607
Butadiene
Molecular form in which substituents on two adjacent atoms are closest together
conformational isomers (conformers), or sometimes rotational isomers (rotamers). Conformations can be described by dihedral angles, which are used to
Eclipsed_conformation
Soil improvement and conservation methodologies
28, 2013.{{cite web}}: CS1 maint: archived copy as title (link) "Camp Rotamer ready to host open house". GazetteXtra. Archived from the original on November
Forestry_mulching
Chemical compound
because of steric interactions due to the branching of the β-carbon. No rotamer of the molecule would allow a backside attack of the α carbon. β-Hydride
Neophyl_chloride
Study of how proteins move and change shape
such as sidechains that jump between separate discrete energy minima, or rotamers. Evidence for local flexibility is often obtained from NMR spectroscopy
Protein_dynamics
Presence of isomers with identical centers of mass in a crystal
arranged in sheets. Disorder is common for molecules where more than one rotamer, conformer, or isomer where the center of mass of each form is identical
Crystallographic_disorder
both conversions occur simultaneously. Contrast irreversible reaction. rotamer round-bottom flask rust Contents: Top 0–9 A B C D E F G H I J K L M N
Glossary_of_chemistry_terms
Chemical compound
average equatorial manganese-carbonyl distance of 185.6 pm. In the stable rotamer, the two Mn(CO)5 subunits are staggered. Thus, the overall molecule has
Dimanganese_decacarbonyl
Prediction method in molecular modeling
conformations are often used to emulate receptor flexibility. Alternatively rotamer libraries of amino acid side chains that surround the binding cavity may
Docking_(molecular)
Chimera Yes Yes Yes No No No No No No Visually appealing viewer, amino acid rotamers and other building, includes Antechamber and MMTK, Ambertools plugins in
Comparison of software for molecular mechanics modeling
Comparison_of_software_for_molecular_mechanics_modeling
Method of protein structure prediction using other known proteins
side-chain conformation for homologous proteins using an energy-based rotamer search". J Mol Biol. 229 (4): 996–1006. doi:10.1006/jmbi.1993.1100. PMID 8445659
Homology_modeling
electrostatics approach, e.g., for considering multiple amino acid sidechain rotamers. In addition, current commonly used molecular force fields do not take
Protein_pKa_calculations
Type of compound having a metal center
Single crystal X-ray diffraction studies reveal both eclipsed or staggered rotamers. For non-substituted metallocenes the energy difference between the staggered
Metallocene
Chemical reaction
Additionally using a solid support restricts conformational movement (rotamer effect). Traditional catalytic aids such as phosphine ligands make the
Pauson–Khand_reaction
Soviet physicist (1922–1980)
established the existence of one molecule (H-propanol) in five non-equivalent rotamer states. In the class of aromatic compounds, Latif Imanov found dielectric
Latif_Imanov
Process of evaluating 3-dimensional atomic models of biomacromolecules
side-chain dihedrals (χ's), one should refer to the Dunbrack Backbone-dependent rotamer library. Though, mRNA structures are generally short-lived and single-stranded
Structure_validation
Bioengineering process
specified design positions, identifying the lowest energy combination of rotamers, and determining whether the new design has a lower binding energy than
Protein_engineering
(steric clash scores), (iv) the distribution of the side-chain conformers (rotamers) and, (v) hydrogen bonding parameters. The advent of the complementarity
Complementarity_plot
automatically infers missing information, e.g., a protein's hydrogens or bonds. A Rotamer Library allows determining, assigning, and switching between a protein's
BALL
on December 2, 2008. "SHARPEN: Systematic Hierarchical Algorithms for Rotamers and Proteins on an Extended Network (deadlink)". Archived from the original
List_of_Folding@home_cores
Chemical compound
(LSD) analogue N-methyl-N-isopropyllysergamide (MiPLA): Insights from Rotamers in NMR spectra". Drug Test Anal. 16 (6): 588–594. doi:10.1002/dta.3586
MiPLA
Bioinformatics subfield
mechanics modeling Protein structure prediction CASP Backbone-dependent rotamer library Gu J, Bourne PE (2011). Structural Bioinformatics (2nd ed.). Hoboken:
Structural_bioinformatics
Pharmaceutical compound
it should not be assumed that "inactive" conformationally constrained rotamers are necessarily pharmacologically inactive; results depend on the similarity
DOB-CR
Chemical compound
is the most stable according to calculations. For HOSSOH, two different rotamers are possible, one with symmetry C1 and the other C2. The sulfur analog
Thiosulfurous_acid
Chemical compound
although it has no or few practical uses. The molecule exists in two rotamers, gauche and anti. The six CO ligands are terminal, and the W-W bond distance
Cyclopentadienyltungsten tricarbonyl dimer
Cyclopentadienyltungsten_tricarbonyl_dimer
Method of analyzing transmission electron microscopy imagery
morphing (shifting and rotation of pieces) and sidechain orientations (rotamers), which is addressed in this step. In more involved cases, a force field
Single_particle_analysis
Coordination compound
η8-tetraenes are 8-electron ligands. Butadiene more commonly binds in its cisoid rotamer, but transoid butadiene ligands have been observed. In both cases, the
Transition metal complexes of dienes, trienes, and tetraenes
Transition_metal_complexes_of_dienes,_trienes,_and_tetraenes
Chemical compound
research although it has no known practical uses. The molecule exists in two rotamers, gauche and anti. The six CO ligands are terminal and the Mo-Mo bond distance
Cyclopentadienylmolybdenum tricarbonyl dimer
Cyclopentadienylmolybdenum_tricarbonyl_dimer
library approach. To model discrete states of a side chain, one could use a rotamer library approach. This approach operates under the assumption that local
Protein_fragment_library
HIV-1 RT makes the p66 thumb domain hyper extended because it induces rotamer conformation changes in amino acid residues Tyr-181 and Tyr-188. This affects
Discovery and development of non-nucleoside reverse-transcriptase inhibitors
Discovery_and_development_of_non-nucleoside_reverse-transcriptase_inhibitors
Type of strain energy in organic chemistry
with an increase in substituent size, the equilibrium enthalpies between rotamers also increases. For example, when examining 4-methyl-2-pentene which contains
Allylic_strain
American computer scientist and computational biologist
flexibility into the design process by using ensembles and continuously flexible rotamers and backbones. Donald has also developed algorithms for determining the
Bruce_Donald
Skin whitening agent
K, Kjaergaard HG, Perry NB, Weavers RT (August 2003). "Hydrogen-bonded rotamers of 2′,4′,6′-trihydroxy-3′-formyldihydrochalcone, an intermediate in the
Linderatin
ROTAMER
ROTAMER
ROTAMER
ROTAMER
Boy/Male
Indian
Silence
Girl/Female
Tamil
Name of a river
Girl/Female
Australian, Greek, Romanian
Farmer
Boy/Male
Hindu
One without sorrow, Happy, Content, Without grief
Boy/Male
Tamil
Somanshu | ஸோமாநà¯à®·à¯
Moonbeam
Surname or Lastname
English
English : from a Germanic personal name composed of the elements geba ‘gift’ + hard ‘hardy’, ‘brave’, ‘strong’ (see Gebhardt).
Girl/Female
Tamil
Poetry in motion
Girl/Female
Indian, Sanskrit
Purifier
Girl/Female
Muslim
Blessings of Allah
Girl/Female
Muslim
An early philanthropic woman
ROTAMER
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ROTAMER
ROTAMER
ROTAMER