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Protocols for Molecular Modeling with Rosetta3 and RosettaScripts

Brian J. Bender, Alberto Cisneros, Amanda M. Duran, Jessica A. Finn, Darwin Fu, Alyssa D. Lokits, Benjamin K. Mueller, Amandeep K. Sangha, Marion F. Sauer, Alexander M. Sevy, Gregory Sliwoski, Jonathan H. Sheehan (+3 others)
<span title="2016-08-16">2016</span> <i title="American Chemical Society (ACS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4qyryvw5mvde5nt6xjruewxve4" style="color: black;">Biochemistry</a> </i> &nbsp;
Previously, we published an article providing an overview of the Rosetta suite of biomacromolecular modeling software and a series of step-by-step tutorials [Kaufmann, K.  ...  , protein docking, small molecule docking, and protein design.  ...  This flexibility has made a number of scientific advances possible, such as de novo design of an influenza binder, 10 proteinprotein docking based on hybrid structural methods, 42 and HIV vaccine design  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/acs.biochem.6b00444">doi:10.1021/acs.biochem.6b00444</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27490953">pmid:27490953</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5007558/">pmcid:PMC5007558</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tyuhowjhxfb2vknzci57dg5gve">fatcat:tyuhowjhxfb2vknzci57dg5gve</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209061924/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5007558&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/76/33/7633508d02d016db739841f8a8d4cd88c4d1a622.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/acs.biochem.6b00444"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acs.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5007558" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Progress in computational protein design

Shaun M. Lippow, Bruce Tidor
<span title="">2007</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/leca7sevx5fbxol36lihhcvvce" style="color: black;">Current Opinion in Biotechnology</a> </i> &nbsp;
Current progress in computational structure-based protein design is reviewed in the areas of methodology and applications.  ...  Foundational advances include new potential functions, more efficient ways of computing energetics, flexible treatments of solvent, and useful energy function approximations, as well as ensemble-based  ...  Acknowledgements This work was supported by a National Science Foundation Graduate Fellowship to S.M.L. and grants from the National Institutes of Health (GM65418 and CA96504).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.copbio.2007.04.009">doi:10.1016/j.copbio.2007.04.009</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17644370">pmid:17644370</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3495006/">pmcid:PMC3495006</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ie2nfuivc5g3jlunubkksqyfei">fatcat:ie2nfuivc5g3jlunubkksqyfei</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20100617223712/http://www.cs.duke.edu/brd/papers/pdf-reprints/tidor-review07.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/81/b3/81b35e83beb0c4dfbfeb6531e7d72f9a8b53d027.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.copbio.2007.04.009"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495006" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A Set of Computationally Designed Orthogonal Antiparallel Homodimers that Expands the Synthetic Coiled-Coil Toolkit

Christopher Negron, Amy E. Keating
<span title="2014-11-13">2014</span> <i title="American Chemical Society (ACS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/czzozsmlgreapacsfn45462e54" style="color: black;">Journal of the American Chemical Society</a> </i> &nbsp;
We tested the ability of the distance-dependent statistical potential DFIRE to predict orientation preferences for coiled-coil dimers of known structure.  ...  structures and functions.  ...  design method development) to A.E.K.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/ja507847t">doi:10.1021/ja507847t</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25337788">pmid:25337788</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4277747/">pmcid:PMC4277747</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pm323gz2qrh47krluvwjsyxlmy">fatcat:pm323gz2qrh47krluvwjsyxlmy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719084221/http://dspace.mit.edu/bitstream/handle/1721.1/110032/Keating_A%20set%20of%20computationally.pdf;jsessionid=AB2DF2DE135081B514B35DCCC35D113F?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d9/8f/d98f3834fa469a45109e9848294fa048276e0f7e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/ja507847t"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acs.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4277747" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

UNRES

Adam Liwo, Stanislaw Oldziej, Harold A. Scheraga, Jaroslaw Pillardy, Cezary Czaplewski, Jooyoung Lee, Daniel R. Ripoll, Malgorzata Groth, Sylwia Rodziewicz-Motowidlo, Rajmund Kamierkiewicz, Ryszard J. Wawak
<span title="">2000</span> <i title="ACM Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/abb3deffcrervb3skz37d67v4m" style="color: black;">Proceedings of the fourth annual international conference on Computational molecular biology - RECOMB &#39;00</a> </i> &nbsp;
Acknowledsements This work was supported by grants from the Na-  ...  in the data base of decoys taken from the PDB), but was not capable of de nolo folding of a protein [22, 24] .  ...  As shown, these terms are dependent not only on the relative orientation of the two peptide groups, but also on the virtual-bond dihedral angles "fl and ~f2 centered on the corresponding C"-C = virtualbond  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/332306.332544">doi:10.1145/332306.332544</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/recomb/LiwoPCLRGRKWOS00.html">dblp:conf/recomb/LiwoPCLRGRKWOS00</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jfvxl3ke5jekpnpwvp7ps4ae7i">fatcat:jfvxl3ke5jekpnpwvp7ps4ae7i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20070824042226/http://www.cs.brown.edu/people/sorin/lab/_proFolding/papers/2000/p193-liwo.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c0/81/c0810ab2674b1a9208bec8aadff59c4a1eb6b474.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/332306.332544"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acm.org </button> </a>

Recent Progress Using De Novo Design to Study Protein Structure, Design and Binding Interactions

Juan Ferrando, Lee A. Solomon
<span title="2021-03-10">2021</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/gbzbhas4rfd5pkn6xglvth3dre" style="color: black;">Life</a> </i> &nbsp;
De novo protein design is a powerful methodology used to study natural functions in an artificial-protein context.  ...  Here, we will review recent examples of de novo design studies on binding reactions for small molecules, nucleic acids, and the formation of protein-protein interactions.  ...  An important aspect of de novo design is that proteins can be used in abiological contexts.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/life11030225">doi:10.3390/life11030225</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33802210">pmid:33802210</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7999464/">pmcid:PMC7999464</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bjaowu45rvb7jdii5zdsstuzrq">fatcat:bjaowu45rvb7jdii5zdsstuzrq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210313104144/https://res.mdpi.com/d_attachment/life/life-11-00225/article_deploy/life-11-00225.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/68/22/6822bdce602ea23f5e367816d2c863fc58529431.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/life11030225"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7999464" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Computational design of protein–ligand interfaces: potential in therapeutic development

Andrew Morin, Jens Meiler, Laura S. Mizoue
<span title="">2011</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/va62z7g5ofgoday6mzmc4uzqgm" style="color: black;">Trends in Biotechnology</a> </i> &nbsp;
This review focuses on recent advances in computational design methods and their application to protein-small molecule binding sites.  ...  It requires a search algorithm that can rapidly sample the vast sequence and conformational space, and a scoring function that can identify low energy designs.  ...  Hydrogen bonds are explicitly considered because the strength of the interaction is dependent on both distance and orientation between donor and acceptor groups.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tibtech.2011.01.002">doi:10.1016/j.tibtech.2011.01.002</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21295366">pmid:21295366</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3749302/">pmcid:PMC3749302</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/c2a2hhtj5fcdhnxizaigzbun34">fatcat:c2a2hhtj5fcdhnxizaigzbun34</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209054250/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3749302&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1d/76/1d76702d26f2ec8bc99fcef63392c4adc449caba.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tibtech.2011.01.002"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3749302" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Rosetta3 [chapter]

Andrew Leaver-Fay, Michael Tyka, Steven M. Lewis, Oliver F. Lange, James Thompson, Ron Jacak, Kristian W. Kaufman, P. Douglas Renfrew, Colin A. Smith, Will Sheffler, Ian W. Davis, Seth Cooper (+20 others)
<span title="">2011</span> <i title="Elsevier"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/q5zjsptkmzct5n2oh2pbd3hrzy" style="color: black;">Methods in Enzymology</a> </i> &nbsp;
We have recently completed a full re-architecturing of the ROSETTA molecular modeling program, generalizing and expanding its existing functionality.  ...  This chapter describes the requirements for our new architecture, justifies the design decisions, sketches out central classes, and highlights a few of the common tasks that the new software can perform  ...  ACKNOWLEDGMENTS This work was funded by NIH and HHMI. OFL was funded by the Human Frontier Science Program.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/b978-0-12-381270-4.00019-6">doi:10.1016/b978-0-12-381270-4.00019-6</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21187238">pmid:21187238</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4083816/">pmcid:PMC4083816</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ptwefykphjch3dcgeb24bgp5ky">fatcat:ptwefykphjch3dcgeb24bgp5ky</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191210062349/http://www.meilerlab.org/index.php/publications/showPublication/pub_id/111" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/62/f3/62f320ac413113a3c44eb98f946544cbb1ac879a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/b978-0-12-381270-4.00019-6"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4083816" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Julia Koehler Leman, Brian D. Weitzner, Steven M. Lewis, Jared Adolf-Bryfogle, Nawsad Alam, Rebecca F. Alford, Melanie Aprahamian, David Baker, Kyle A. Barlow, Patrick Barth, Benjamin Basanta, Brian J. Bender (+96 others)
<span title="2020-06-01">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/l6cw2tyvgrhytbvantrj2os37y" style="color: black;">Nature Methods</a> </i> &nbsp;
The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide.  ...  We discuss improvements to the score function, user interfaces and usability. Rosetta is available at http://www.rosettacommons.org.  ...  toolkit 147 : mp_score, mp_transform, mp_mutate_relax, helix_from_sequence Jeffrey Gray, Richard Bonneau mp_lipid_acc 148 Richard Bonneau mp_domain_assembly 149 Richard Bonneau RosettaCM for membrane proteins  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41592-020-0848-2">doi:10.1038/s41592-020-0848-2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32483333">pmid:32483333</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7603796/">pmcid:PMC7603796</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wmspe6dzm5andneitqur5lpniy">fatcat:wmspe6dzm5andneitqur5lpniy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200709211216/https://www.preprints.org/manuscript/201904.0263/v3/download" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/7d/5d/7d5d58f56bfa04a5a356da381e313bbfecbd657d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41592-020-0848-2"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7603796" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Chemical Space Expansion of Bromodomain Ligands Guided by in Silico Virtual Couplings (AutoCouple)

Laurent Batiste, Andrea Unzue, Aymeric Dolbois, Fabrice Hassler, Xuan Wang, Nicholas Deerain, Jian Zhu, Dimitrios Spiliotopoulos, Cristina Nevado, Amedeo Caflisch
<span title="2018-02-07">2018</span> <i title="American Chemical Society (ACS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3qlufbxyhnaqljdbzr3sgsf2yq" style="color: black;">ACS Central Science</a> </i> &nbsp;
Here, we present AutoCouple, a de novo approach to computational ligand design focused on the diversity-oriented generation of chemical entities via virtual couplings.  ...  The binding mode was confirmed by X-ray crystallography, target engagement in cells was demonstrated, and antiproliferative activity was showcased in three cancer cell lines.  ...  ■ CONCLUSIONS A de novo design approach based on virtual chemical reactions starting from commercially available building blocks (Auto-Couple) has been developed and successfully applied to the identification  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/acscentsci.7b00401">doi:10.1021/acscentsci.7b00401</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29532017">pmid:29532017</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5833004/">pmcid:PMC5833004</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2u4efk77urd4lefqj3ktbhk2i4">fatcat:2u4efk77urd4lefqj3ktbhk2i4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190428034108/http://discovery.ucl.ac.uk/10063487/1/acscentsci.7b00401.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/cc/89/cc89a61fc230964f8d8c9e3337c4dda0d9eaecc2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/acscentsci.7b00401"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> acs.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5833004" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Recent improvements in prediction of protein structure by global optimization of a potential energy function

J. Pillardy, C. Czaplewski, A. Liwo, J. Lee, D. R. Ripoll, R. Kazmierkiewicz, S. Oldziej, W. J. Wedemeyer, K. D. Gibson, Y. A. Arnautova, J. Saunders, Y.-J. Ye (+1 others)
<span title="2001-02-20">2001</span> <i title="Proceedings of the National Academy of Sciences"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nvtuoas5pbdsllkntnhizy4f4q" style="color: black;">Proceedings of the National Academy of Sciences of the United States of America</a> </i> &nbsp;
The united-residue energy function used in this procedure includes multibody interactions from a cumulant expansion of the free energy of polypeptide chains, with their relative weights determined by Z-score  ...  Recent improvements of a hierarchical ab initio or de novo approach for predicting both ␣ and ␤ structures of proteins are described.  ...  Academic Network (IC MAN) in Gdańsk; and (iv) with our own array of 55 dual-processor PC computers.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.041609598">doi:10.1073/pnas.041609598</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11226239">pmid:11226239</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC30138/">pmcid:PMC30138</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qek2bkxhpjgavj6sah763aqhcq">fatcat:qek2bkxhpjgavj6sah763aqhcq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20081002144307/http://www.mat.univie.ac.at/~neum/glopt/mss/PilCL00.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/db/93/db9331d5c1eaacbc45f585386e42d812645ad02c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.041609598"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC30138" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Coiled coil protein origami: from modular design principles towards biotechnological applications

Fabio Lapenta, Jana Aupič, Žiga Strmšek, Roman Jerala
<span title="">2018</span> <i title="Royal Society of Chemistry (RSC)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qoebttzoxbfgviecxmhjrua4eu" style="color: black;">Chemical Society Reviews</a> </i> &nbsp;
This review illustrates the current state in designing coiled-coil-based proteins with an emphasis on coiled coil protein origami structures and their potential.  ...  Keating kindly provided the models used in Fig. 2a and b. Notes and references  ...  J. and F. L.) and the ERANET SynBio project Bioorigami (ERASYNBIO1-006) and COST action CM1306. Dr Prof. B. Bromley, Dr L. Small and Dr Prof. A.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/c7cs00822h">doi:10.1039/c7cs00822h</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29400389">pmid:29400389</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hh5zyocwrvhblnwftvjgnetobq">fatcat:hh5zyocwrvhblnwftvjgnetobq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200321215822/https://pubs.rsc.org/en/content/articlepdf/2018/cs/c7cs00822h" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/bd/e9/bde9aa10adec62c4198ada0b190b6cd553dcf70a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/c7cs00822h"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico

Aron Broom, Rojo V Rakotoharisoa, Michael C Thompson, Niayesh Zarifi, Erin Nguyen, Nurzhan Mukhametzhanov, Lin Liu, James S Fraser, Roberto A Chica
<span title="2020-09-23">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a4wan6l5o5dfzn767kyz7jqevi" style="color: black;">Nature Communications</a> </i> &nbsp;
Based on these observations, we engineer HG4, an efficient biocatalyst (kcat/KM 103,000 M-1s-1) containing key first and second-shell mutations found during evolution.  ...  Although de novo enzymes have been successfully designed, these exhibit low catalytic efficiencies, requiring directed evolution to improve activity.  ...  hydrogen bond term with a well depth of 8.0 kcal mol −1 and an equilibrium donor-acceptor distance of 2.8 Å 51 , an electrostatic energy term modeled using Coulomb's law with a distance-dependent dielectric  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-020-18619-x">doi:10.1038/s41467-020-18619-x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32968058">pmid:32968058</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7511930/">pmcid:PMC7511930</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xdtn5mnja5ck7iy7utwf5vcmmm">fatcat:xdtn5mnja5ck7iy7utwf5vcmmm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210428104806/https://escholarship.org/content/qt0z88f0sj/qt0z88f0sj.pdf?t=qm5bnc" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8a/c4/8ac4da8e0985715304e6d8a02330da7a59d0d247.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-020-18619-x"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7511930" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Protein structure refinement by optimization

Martin Carlsen, Peter Røgen
<span title="2015-07-21">2015</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fkowqlvuffe5lnyfwblj3fcp7i" style="color: black;">Proteins: Structure, Function, and Bioinformatics</a> </i> &nbsp;
structure, is designed to have native-decoy energy gabs that correlates maximally to a native-decoy distance.  ...  The folding problem is solved using de novo methods or comparative methods depending on whether the three-dimensional structure of a homologous sequence is known.  ...  For each training the negative eigenvalues of the Hessian and the norm of the gradient for all 20 proteins are illustrated in Fig. 8.1a and 8 .1b.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.24846">doi:10.1002/prot.24846</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26095680">pmid:26095680</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qa7zed4qcbah3jlonecncylyq4">fatcat:qa7zed4qcbah3jlonecncylyq4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170923201543/http://orbit.dtu.dk/files/123428834/phd376_Carlsen_M.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/bb/59/bb59dedd6d94fa1ae075e1f6f444dbf9cfe558f2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.24846"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Engineered Proteins: Redox Properties and Their Applications

Shradha Prabhulkar, Hui Tian, Xiaotang Wang, Jun-Jie Zhu, Chen-Zhong Li
<span title="2012-12-15">2012</span> <i title="Mary Ann Liebert Inc"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3a2u75wo7zfhzlnbmwvt4iazt4" style="color: black;">Antioxidants and Redox Signaling</a> </i> &nbsp;
of native proteins by de novo design.  ...  This review presents a selection of engineered redox proteins achieved through these methods, resulting in a manipulation in redox potentials, an increase in electron-transfer efficiency, and an expansion  ...  as de novo metalloproteins and enzymes.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1089/ars.2011.4001">doi:10.1089/ars.2011.4001</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22435347">pmid:22435347</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3474195/">pmcid:PMC3474195</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4ssnwlkurrb3jkz523s77jfxgy">fatcat:4ssnwlkurrb3jkz523s77jfxgy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200208202723/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3474195&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/dd/28/dd284a9e6b3a422d3eb174cc7f5b7195f8a10fca.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1089/ars.2011.4001"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3474195" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Combinatorial methods for small-molecule placement in computational enzyme design

J. K. Lassila, H. K. Privett, B. D. Allen, S. L. Mayo
<span title="2006-10-30">2006</span> <i title="Proceedings of the National Academy of Sciences"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nvtuoas5pbdsllkntnhizy4f4q" style="color: black;">Proceedings of the National Academy of Sciences of the United States of America</a> </i> &nbsp;
de novo computational enzyme design efforts for some time.  ...  Standard backbone-dependent and -independent rotamer libraries were used with expansion by 1 SD about 1 and 2 (17) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.0607691103">doi:10.1073/pnas.0607691103</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17075051">pmid:17075051</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1636520/">pmcid:PMC1636520</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/e4y3cogimjbipipxtva6oiaebm">fatcat:e4y3cogimjbipipxtva6oiaebm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170815162721/http://authors.library.caltech.edu/9967/1/LASpnas06.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/89/35/89351d3c71297872c7d9fdb05f839b71b69fccbd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.0607691103"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636520" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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