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</div> </div> </div> </div> </div> </nav> </div> </div> </div> <div class="vector-column-end"> <div class="vector-sticky-pinned-container"> <nav class="vector-page-tools-landmark" aria-label="Page tools"> <div id="vector-page-tools-pinned-container" class="vector-pinned-container"> </div> </nav> <nav class="vector-appearance-landmark" aria-label="Appearance"> <div id="vector-appearance-pinned-container" class="vector-pinned-container"> <div id="vector-appearance" class="vector-appearance vector-pinnable-element"> <div class="vector-pinnable-header vector-appearance-pinnable-header vector-pinnable-header-pinned" data-feature-name="appearance-pinned" data-pinnable-element-id="vector-appearance" data-pinned-container-id="vector-appearance-pinned-container" data-unpinned-container-id="vector-appearance-unpinned-container" > <div class="vector-pinnable-header-label">Appearance</div> <button class="vector-pinnable-header-toggle-button vector-pinnable-header-pin-button" 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href="/wiki/File:Serine_backbone-dependent_chi1_rotamer_populations.png" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/c/c9/Serine_backbone-dependent_chi1_rotamer_populations.png/220px-Serine_backbone-dependent_chi1_rotamer_populations.png" decoding="async" width="220" height="80" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/c/c9/Serine_backbone-dependent_chi1_rotamer_populations.png/330px-Serine_backbone-dependent_chi1_rotamer_populations.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/c/c9/Serine_backbone-dependent_chi1_rotamer_populations.png/440px-Serine_backbone-dependent_chi1_rotamer_populations.png 2x" data-file-width="4123" data-file-height="1501" /></a><figcaption><b>Backbone-dependent rotamer library for serine</b>. Each plot shows the population of the χ<sub>1</sub> rotamers of serine as a function of the backbone dihedral angles φ and ψ</figcaption></figure> <p>In <a href="/wiki/Biochemistry" title="Biochemistry">biochemistry</a>, a <b>backbone-dependent rotamer library</b> provides the frequencies, mean <a href="/wiki/Dihedral_angles" class="mw-redirect" title="Dihedral angles">dihedral angles</a>, and standard deviations of the discrete conformations (known as <a href="/wiki/Rotamer" title="Rotamer">rotamers</a>) of the <a href="/wiki/Amino_acid" title="Amino acid">amino acid</a> <a href="/wiki/Side_chain#Biochemistry" title="Side chain">side chains</a> in <a href="/wiki/Protein" title="Protein">proteins</a> as a function of the <a href="/wiki/Protein_backbone" class="mw-redirect" title="Protein backbone">backbone</a> <a href="/wiki/Dihedral_angle" title="Dihedral angle">dihedral angles</a> φ and ψ of the <a href="/wiki/Ramachandran_plot" title="Ramachandran plot">Ramachandran map</a>. By contrast, backbone-independent rotamer libraries express the frequencies and mean dihedral angles for all side chains in proteins, regardless of the backbone conformation of each residue type. Backbone-dependent rotamer libraries have been shown to have significant advantages over backbone-independent rotamer libraries, principally when used as an energy term, by speeding up search times of side-chain packing algorithms used in <a href="/wiki/Protein_structure_prediction" title="Protein structure prediction">protein structure prediction</a> and <a href="/wiki/Protein_design" title="Protein design">protein design</a>.<sup id="cite_ref-HPZ2020_1-0" class="reference"><a href="#cite_note-HPZ2020-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup> </p> <meta property="mw:PageProp/toc" /> <div class="mw-heading mw-heading2"><h2 id="History">History</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Backbone-dependent_rotamer_library&action=edit&section=1" title="Edit section: History"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The first backbone-dependent rotamer library was developed in 1993 by <a href="/w/index.php?title=Roland_Dunbrack&action=edit&redlink=1" class="new" title="Roland Dunbrack (page does not exist)">Roland Dunbrack</a> and <a href="/wiki/Martin_Karplus" title="Martin Karplus">Martin Karplus</a> to assist the prediction of the Cartesian coordinates of a protein's side chains given the experimentally determined or predicted Cartesian coordinates of its main chain.<sup id="cite_ref-DK1993_2-0" class="reference"><a href="#cite_note-DK1993-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> The library was derived from the structures of 132 proteins from the <a href="/wiki/Protein_Data_Bank" title="Protein Data Bank">Protein Data Bank</a> with <a href="/wiki/Resolution_(electron_density)" class="mw-redirect" title="Resolution (electron density)">resolution</a> of 2.0 <a href="/wiki/Angstrom" title="Angstrom">Å</a> or better. The library provided the counts and frequencies of χ<sub>1</sub> or χ<sub>1</sub>+χ<sub>2</sub> rotamers of 18 amino acids (excluding <a href="/wiki/Glycine" title="Glycine">glycine</a> and <a href="/wiki/Alanine" title="Alanine">alanine</a> residue types, since they do not have a χ<sub>1</sub> dihedral) for each 20° x 20° bin of the Ramachandran map (φ,ψ = -180° to -160°, -160° to -140° etc.). </p><p>In 1997, Dunbrack and <a href="/w/index.php?title=Fred_E._Cohen&action=edit&redlink=1" class="new" title="Fred E. Cohen (page does not exist)">Fred E. Cohen</a> at the <a href="/wiki/University_of_California,_San_Francisco" title="University of California, San Francisco">University of California, San Francisco</a> presented a backbone-dependent rotamer library derived from <a href="/wiki/Bayesian_statistics" title="Bayesian statistics">Bayesian statistics</a>.<sup id="cite_ref-DC1997_3-0" class="reference"><a href="#cite_note-DC1997-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup> The Bayesian approach provided the opportunity for the definition of a Bayesian prior for the frequencies of rotamers in each 10° x 10° bin derived by assuming that the steric and electrostatic effects of the φ and ψ dihedral angles are independent. In addition, a periodic kernel with 180° periodicity was used to count side chains 180° away in each direction from the bin of interest. As an exponent of a sin<sup>2</sup> function, it behaved much like a <a href="/wiki/Von_Mises_distribution" title="Von Mises distribution">von Mises distribution</a> commonly used in <a href="/wiki/Directional_statistics" title="Directional statistics">directional statistics</a>. The 1997 library was made publicly available via the World Wide Web in 1997, and found early use in <a href="/wiki/Protein_structure_prediction" title="Protein structure prediction">protein structure prediction</a><sup id="cite_ref-BCD1997_4-0" class="reference"><a href="#cite_note-BCD1997-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> and <a href="/wiki/Protein_design" title="Protein design">protein design</a>.<sup id="cite_ref-KB2000_5-0" class="reference"><a href="#cite_note-KB2000-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup> The library derived from Bayesian statistics was updated in 2002<sup id="cite_ref-D2002_6-0" class="reference"><a href="#cite_note-D2002-6"><span class="cite-bracket">[</span>6<span class="cite-bracket">]</span></a></sup> </p> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Phenylalanine_backbone-dependent_chi1_rotamer_populations.png" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/f/f1/Phenylalanine_backbone-dependent_chi1_rotamer_populations.png/220px-Phenylalanine_backbone-dependent_chi1_rotamer_populations.png" decoding="async" width="220" height="80" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/f/f1/Phenylalanine_backbone-dependent_chi1_rotamer_populations.png/330px-Phenylalanine_backbone-dependent_chi1_rotamer_populations.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/f/f1/Phenylalanine_backbone-dependent_chi1_rotamer_populations.png/440px-Phenylalanine_backbone-dependent_chi1_rotamer_populations.png 2x" data-file-width="4130" data-file-height="1500" /></a><figcaption><b>Backbone-dependent rotamer library for phenylalanine</b>. Each plot shows the population of the χ<sub>1</sub> rotamers of phenylalanine as a function of the backbone dihedral angles φ and ψ</figcaption></figure> <p>Many modeling programs, such as <a href="/wiki/Rosetta@Home" class="mw-redirect" title="Rosetta@Home">Rosetta</a>, use a backbone-dependent rotamer library as a scoring function (usually in the form E=-ln(p(rotamer(<i>i</i>) | φ,ψ)) for the <i>i</i>th rotamer, and optimize the backbone conformation of proteins by minimizing the rotamer energy with derivatives of the log probabilities with respect to φ,ψ.<sup id="cite_ref-AG2017_7-0" class="reference"><a href="#cite_note-AG2017-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup> This requires smooth probability functions with smooth derivatives, because most <a href="/wiki/Mathematical_optimization" title="Mathematical optimization">mathematical optimization</a> algorithms use first and sometimes second derivatives and will get stuck in local minima on rough surfaces. In 2011, Shapovalov and Dunbrack published a smoothed backbone-dependent rotamer library derived from kernel density estimates and kernel regressions with <a href="/wiki/Von_Mises_distribution" title="Von Mises distribution">von Mises distribution</a> kernels on the φ,ψ variables.<sup id="cite_ref-SD2011_8-0" class="reference"><a href="#cite_note-SD2011-8"><span class="cite-bracket">[</span>8<span class="cite-bracket">]</span></a></sup> The treatment of the non-rotameric degrees of freedom (those dihedral angles not about <a href="/wiki/Orbital_hybridisation" title="Orbital hybridisation">sp<sup>3</sup>-sp<sup>3</sup> bonds</a>, such as <a href="/wiki/Asparagine" title="Asparagine">asparagine</a> and <a href="/wiki/Aspartate" class="mw-redirect" title="Aspartate">aspartate</a> χ<sub>2</sub>, <a href="/wiki/Phenylalanine" title="Phenylalanine">phenylalanine</a>, <a href="/wiki/Tyrosine" title="Tyrosine">tyrosine</a>, <a href="/wiki/Histidine" title="Histidine">histidine</a>, <a href="/wiki/Tryptophan" title="Tryptophan">tryptophan</a> χ<sub>2</sub>, and <a href="/wiki/Glutamine" title="Glutamine">glutamine</a> and <a href="/wiki/Glutamate" class="mw-redirect" title="Glutamate">glutamate</a> χ<sub>3</sub>) was improved by modeling the dihedral angle <a href="/wiki/Probability_density" class="mw-redirect" title="Probability density">probability density</a> of each of these dihedral angles as a function of χ<sub>1</sub> rotamer (or χ<sub>1</sub> and χ<sub>2</sub> for Gln and Glu) and φ,ψ. The functions are essentially regressions of a periodic probability density on a <a href="/wiki/Torus" title="Torus">torus</a>. </p><p>In addition to statistical analysis of structures in the <a href="/wiki/Protein_Data_Bank" title="Protein Data Bank">Protein Data Bank</a>, backbone-dependent rotamer libraries can also be derived from <a href="/wiki/Molecular_dynamics" title="Molecular dynamics">molecular dynamics</a> simulations of proteins, as demonstrated by the Dynameomics Library from <a href="/wiki/Valerie_Daggett" title="Valerie Daggett">Valerie Daggett</a>'s research group.<sup id="cite_ref-TD2016_9-0" class="reference"><a href="#cite_note-TD2016-9"><span class="cite-bracket">[</span>9<span class="cite-bracket">]</span></a></sup> Because these libraries are based on sampling from simulations, they can generate far larger numbers of data points across regions of the Ramachandran map that are sparsely populated in experimental structures, leading to higher statistical significance in these regions. Rotamer libraries derived from simulations are dependent on the <a href="/wiki/Force_field_(chemistry)" title="Force field (chemistry)">force field</a> used in the simulations. The Dynameomics Library is built on simulations using the ENCAD force field of Levitt et al. from 1995.<sup id="cite_ref-LD1995_10-0" class="reference"><a href="#cite_note-LD1995-10"><span class="cite-bracket">[</span>10<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="Backbone-dependence_of_rotamer_populations">Backbone-dependence of rotamer populations</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Backbone-dependent_rotamer_library&action=edit&section=2" title="Edit section: Backbone-dependence of rotamer populations"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:BBDEP_Newman_diagram.png" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/7/7c/BBDEP_Newman_diagram.png/220px-BBDEP_Newman_diagram.png" decoding="async" width="220" height="179" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/7/7c/BBDEP_Newman_diagram.png/330px-BBDEP_Newman_diagram.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/7/7c/BBDEP_Newman_diagram.png/440px-BBDEP_Newman_diagram.png 2x" data-file-width="7447" data-file-height="6050" /></a><figcaption>Steric interactions that affect the backbone-conformation-dependent rotamer preferences of amino acid side chains, shown in a <a href="/wiki/Newman_projection" title="Newman projection">Newman projection</a> </figcaption></figure> <p>The effect of backbone conformation on side-chain rotamer frequencies is primarily due to <a href="/wiki/Steric_repulsion" class="mw-redirect" title="Steric repulsion">steric repulsions</a> between backbone atoms whose position is dependent on φ and ψ and the side-chain γ heavy atoms (carbon, oxygen, or sulfur) of each residue type (PDB atom types CG, CG1, CG2, OG, OG1, SG). These occur in predictable combinations that depend on the dihedrals connecting the backbone atoms to the side-chain atoms.<sup id="cite_ref-DK1994_11-0" class="reference"><a href="#cite_note-DK1994-11"><span class="cite-bracket">[</span>11<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-DC1997_3-1" class="reference"><a href="#cite_note-DC1997-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup> These steric interactions occur when the connecting dihedral angles form a pair of dihedral angles with values {-60°,+60°} or {+60°,-60°}, in a manner related to the phenomenon of <a href="/wiki/Pentane_interference" title="Pentane interference">pentane interference</a>. For example, the nitrogen atom of residue i+1 is connected to the γ heavy atom of any side chain by a connected set of 5 atoms: N(i+1)-C(i)-Cα(i)-Cβ(i)-Cγ(i). The dihedral angle N(i+1)-C(i)-Cα(i)-Cβ(i) is equal to ψ+120°, and C(i)-Cα(i)-Cβ(i)-Cγ(i) is equal to χ<sub>1</sub>-120°. When ψ is -60° and χ<sub>1</sub> is +60° (the g+ rotamer of a side chain), there is a steric interaction between N(i+1) and Cγ because the dihedral angles connecting them are N(i+1)-C(i)-Cα(i)-Cβ(i) = ψ+120° = +60°, and C(i)-Cα(i)-Cβ(i)-Cγ(i) = χ<sub>1</sub>-120° = -60°. The same interaction occurs when ψ is 0° and χ<sub>1</sub> is 180° (the trans rotamer of a side chain). The carbonyl oxygen of residue i plays the same role when ψ=-60° for the g+ rotamer and when ψ=180° for the trans rotamer. Finally, φ-dependent interactions occur between the side-chain γ heavy atoms in g- and g+ rotamers on the one hand, and the carbonyl carbon of residue i-1 and a γ heavy atom, and between the backbone NH of residue i and its hydrogen-bonding partner on the other. </p> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:LYS_Chi1_RamaPlots_SynPentane_interactions.png" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/e/e8/LYS_Chi1_RamaPlots_SynPentane_interactions.png/220px-LYS_Chi1_RamaPlots_SynPentane_interactions.png" decoding="async" width="220" height="105" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/e/e8/LYS_Chi1_RamaPlots_SynPentane_interactions.png/330px-LYS_Chi1_RamaPlots_SynPentane_interactions.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/e/e8/LYS_Chi1_RamaPlots_SynPentane_interactions.png/440px-LYS_Chi1_RamaPlots_SynPentane_interactions.png 2x" data-file-width="2795" data-file-height="1330" /></a><figcaption>Side-chain/main-chain steric interactions that affect the Ramachandran plot distributions of amino acids. The data are for the amino acid lysine</figcaption></figure> <p>The φ,ψ-dependent interactions of backbone atoms and side-chain Cγ atoms can be observed in the distribution of observations in the <a href="/wiki/Ramachandran_plot" title="Ramachandran plot">Ramachandran plot</a> of each χ<sub>1</sub> rotamer (marked in the figure). At these positions, the Ramachandran populations of the rotamers are significantly reduced. They can be summarized as follows: </p> <table class="wikitable" style="text-align: center; margin-left: auto; margin-right: auto"> <caption>φ,ψ-dependence of backbone/side-chain interactions </caption> <tbody><tr> <th>Rotamer</th> <th>N(i+1)</th> <th>O(i) </th></tr> <tr> <td>g+</td> <td>ψ = -60°</td> <td>ψ = +120° </td></tr> <tr> <td>trans</td> <td>ψ = 180°</td> <td>ψ = 0° </td></tr> <tr> <th>Rotamer</th> <th>C(i-1)</th> <th>HBond to NH(i) </th></tr> <tr> <td>g+</td> <td>φ = +60°</td> <td>φ = -120° </td></tr> <tr> <td>g-</td> <td>φ = -180°</td> <td>φ = 0° </td></tr></tbody></table> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Valine_backbone-dependent_chi1_rotamer_populations.png" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/c/ce/Valine_backbone-dependent_chi1_rotamer_populations.png/220px-Valine_backbone-dependent_chi1_rotamer_populations.png" decoding="async" width="220" height="80" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/c/ce/Valine_backbone-dependent_chi1_rotamer_populations.png/330px-Valine_backbone-dependent_chi1_rotamer_populations.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/c/ce/Valine_backbone-dependent_chi1_rotamer_populations.png/440px-Valine_backbone-dependent_chi1_rotamer_populations.png 2x" data-file-width="4150" data-file-height="1501" /></a><figcaption><b>Backbone-dependent rotamer library for valine</b>. Each plot shows the population of the χ<sub>1</sub> rotamers of valine as a function of the backbone dihedral angles φ and ψ</figcaption></figure> <p>Side-chain types with two heavy atoms (Val, Ile, Thr) have backbone-dependent interactions with both heavy atoms. Val has CG1 at χ<sub>1</sub> and CG2 at χ<sub>1</sub>+120°. Because Val g+ and g- conformations have steric interactions with the backbone near ψ=120° and -60° (the most populated ψ ranges), Val is the only amino acid where the t rotamer (χ<sub>1</sub>~180°) is the most common. At most values of φ and ψ, only one rotamer of Val is allowed (shown in figure). Ile has CG1 at χ<sub>1</sub> and CG2 at χ<sub>1</sub>-120°. Thr has OG1 at χ<sub>1</sub> and CG2 at χ<sub>1</sub>-120°. </p> <div class="mw-heading mw-heading2"><h2 id="Uses">Uses</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Backbone-dependent_rotamer_library&action=edit&section=3" title="Edit section: Uses"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The Dunbrack backbone-dependent rotamer library is used in a number of programs for protein structure prediction and computational design, including: </p> <ul><li>Side-chain conformation prediction in protein structure modeling <ul><li><a href="/wiki/Swiss-model" title="Swiss-model">Swiss-model</a><sup id="cite_ref-WS2018_12-0" class="reference"><a href="#cite_note-WS2018-12"><span class="cite-bracket">[</span>12<span class="cite-bracket">]</span></a></sup> and its software, ProMod3<sup id="cite_ref-SS2021_13-0" class="reference"><a href="#cite_note-SS2021-13"><span class="cite-bracket">[</span>13<span class="cite-bracket">]</span></a></sup></li> <li><a href="/wiki/Rosetta@home" title="Rosetta@home">Rosetta</a><sup id="cite_ref-AG2017_7-1" class="reference"><a href="#cite_note-AG2017-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup></li> <li><a href="/wiki/I-TASSER" title="I-TASSER">I-TASSER</a></li> <li><a href="/wiki/Phyre" title="Phyre">Phyre</a><sup id="cite_ref-KS2015_14-0" class="reference"><a href="#cite_note-KS2015-14"><span class="cite-bracket">[</span>14<span class="cite-bracket">]</span></a></sup></li> <li><a href="/wiki/OpenEye_Scientific_Software" title="OpenEye Scientific Software">OEChem TK</a><sup id="cite_ref-OEC2020_15-0" class="reference"><a href="#cite_note-OEC2020-15"><span class="cite-bracket">[</span>15<span class="cite-bracket">]</span></a></sup></li> <li><a href="/wiki/YASARA" title="YASARA">YASARA</a><sup id="cite_ref-EK2009_16-0" class="reference"><a href="#cite_note-EK2009-16"><span class="cite-bracket">[</span>16<span class="cite-bracket">]</span></a></sup></li> <li><a rel="nofollow" class="external text" href="http://seoklab.github.io/GalaxyRefine/">GalaxyRefine</a><sup id="cite_ref-HPS2013_17-0" class="reference"><a href="#cite_note-HPS2013-17"><span class="cite-bracket">[</span>17<span class="cite-bracket">]</span></a></sup></li> <li><a rel="nofollow" class="external text" href="http://dunbrack.fccc.edu/lab/scwrl">SCWRL4</a><sup id="cite_ref-KSD2009_18-0" class="reference"><a href="#cite_note-KSD2009-18"><span class="cite-bracket">[</span>18<span class="cite-bracket">]</span></a></sup></li></ul></li></ul> <ul><li>Protein Design <ul><li><a href="/wiki/Rosetta@home" title="Rosetta@home">Rosetta</a><sup id="cite_ref-AG2017_7-2" class="reference"><a href="#cite_note-AG2017-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup></li> <li><a rel="nofollow" class="external text" href="https://zhanglab.ccmb.med.umich.edu/EvoEF/">EvoEF2</a><sup id="cite_ref-HZ2020_19-0" class="reference"><a href="#cite_note-HZ2020-19"><span class="cite-bracket">[</span>19<span class="cite-bracket">]</span></a></sup></li></ul></li></ul> <ul><li>Visualization of Protein Mutations <ul><li><a href="/wiki/PyMol" class="mw-redirect" title="PyMol">PyMol</a><sup id="cite_ref-DWK2010_20-0" class="reference"><a href="#cite_note-DWK2010-20"><span class="cite-bracket">[</span>20<span class="cite-bracket">]</span></a></sup></li> <li><a href="/wiki/UCSF_Chimera" title="UCSF Chimera">UCSF Chimera</a><sup id="cite_ref-CX2021_21-0" class="reference"><a href="#cite_note-CX2021-21"><span class="cite-bracket">[</span>21<span class="cite-bracket">]</span></a></sup></li></ul></li></ul> <div class="mw-heading mw-heading2"><h2 id="References">References</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Backbone-dependent_rotamer_library&action=edit&section=4" title="Edit section: References"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <style data-mw-deduplicate="TemplateStyles:r1239543626">.mw-parser-output .reflist{margin-bottom:0.5em;list-style-type:decimal}@media screen{.mw-parser-output .reflist{font-size:90%}}.mw-parser-output .reflist .references{font-size:100%;margin-bottom:0;list-style-type:inherit}.mw-parser-output .reflist-columns-2{column-width:30em}.mw-parser-output .reflist-columns-3{column-width:25em}.mw-parser-output .reflist-columns{margin-top:0.3em}.mw-parser-output .reflist-columns ol{margin-top:0}.mw-parser-output .reflist-columns li{page-break-inside:avoid;break-inside:avoid-column}.mw-parser-output .reflist-upper-alpha{list-style-type:upper-alpha}.mw-parser-output .reflist-upper-roman{list-style-type:upper-roman}.mw-parser-output .reflist-lower-alpha{list-style-type:lower-alpha}.mw-parser-output .reflist-lower-greek{list-style-type:lower-greek}.mw-parser-output .reflist-lower-roman{list-style-type:lower-roman}</style><div class="reflist"> <div class="mw-references-wrap mw-references-columns"><ol class="references"> <li id="cite_note-HPZ2020-1"><span class="mw-cite-backlink"><b><a href="#cite_ref-HPZ2020_1-0">^</a></b></span> <span class="reference-text"><style data-mw-deduplicate="TemplateStyles:r1238218222">.mw-parser-output cite.citation{font-style:inherit;word-wrap:break-word}.mw-parser-output .citation q{quotes:"\"""\"""'""'"}.mw-parser-output .citation:target{background-color:rgba(0,127,255,0.133)}.mw-parser-output .id-lock-free.id-lock-free a{background:url("//upload.wikimedia.org/wikipedia/commons/6/65/Lock-green.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-limited.id-lock-limited a,.mw-parser-output .id-lock-registration.id-lock-registration a{background:url("//upload.wikimedia.org/wikipedia/commons/d/d6/Lock-gray-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-subscription.id-lock-subscription a{background:url("//upload.wikimedia.org/wikipedia/commons/a/aa/Lock-red-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .cs1-ws-icon a{background:url("//upload.wikimedia.org/wikipedia/commons/4/4c/Wikisource-logo.svg")right 0.1em center/12px no-repeat}body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-free a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-limited a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-registration a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-subscription a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .cs1-ws-icon a{background-size:contain;padding:0 1em 0 0}.mw-parser-output .cs1-code{color:inherit;background:inherit;border:none;padding:inherit}.mw-parser-output .cs1-hidden-error{display:none;color:var(--color-error,#d33)}.mw-parser-output .cs1-visible-error{color:var(--color-error,#d33)}.mw-parser-output .cs1-maint{display:none;color:#085;margin-left:0.3em}.mw-parser-output .cs1-kern-left{padding-left:0.2em}.mw-parser-output .cs1-kern-right{padding-right:0.2em}.mw-parser-output .citation .mw-selflink{font-weight:inherit}@media screen{.mw-parser-output .cs1-format{font-size:95%}html.skin-theme-clientpref-night .mw-parser-output .cs1-maint{color:#18911f}}@media screen and (prefers-color-scheme:dark){html.skin-theme-clientpref-os .mw-parser-output .cs1-maint{color:#18911f}}</style><cite id="CITEREFHuangPearceZhang2020" class="citation journal cs1">Huang, X; Pearce, R; Zhang, Y (2020). <a rel="nofollow" class="external text" href="https://par.nsf.gov/servlets/purl/10167312">"Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries"</a>. <i>Journal of Chemical Information and Modeling</i>. <b>60</b> (1): <span class="nowrap">410–</span>420. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1021%2Facs.jcim.9b00812">10.1021/acs.jcim.9b00812</a>. <a href="/wiki/PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7938712">7938712</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/31851497">31851497</a><span class="reference-accessdate">. Retrieved <span class="nowrap">18 February</span> 2021</span>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Journal+of+Chemical+Information+and+Modeling&rft.atitle=Toward+the+Accuracy+and+Speed+of+Protein+Side-Chain+Packing%3A+A+Systematic+Study+on+Rotamer+Libraries.&rft.volume=60&rft.issue=1&rft.pages=%3Cspan+class%3D%22nowrap%22%3E410-%3C%2Fspan%3E420&rft.date=2020&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC7938712%23id-name%3DPMC&rft_id=info%3Apmid%2F31851497&rft_id=info%3Adoi%2F10.1021%2Facs.jcim.9b00812&rft.aulast=Huang&rft.aufirst=X&rft.au=Pearce%2C+R&rft.au=Zhang%2C+Y&rft_id=https%3A%2F%2Fpar.nsf.gov%2Fservlets%2Fpurl%2F10167312&rfr_id=info%3Asid%2Fen.wikipedia.org%3ABackbone-dependent+rotamer+library" class="Z3988"></span></span> </li> <li id="cite_note-DK1993-2"><span class="mw-cite-backlink"><b><a href="#cite_ref-DK1993_2-0">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222" /><cite id="CITEREFDunbrackKarplus1993" class="citation journal cs1">Dunbrack, RL Jr.; Karplus, M (1993). 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