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Ab initiomolecular-replacement phasing for symmetric helical membrane proteins

Pavel Strop, Michael R. Brzustowicz, Axel T. Brunger
<span title="2007-01-16">2007</span> <i title="International Union of Crystallography (IUCr)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6inoqqfovnhtledhw3uuo322xa" style="color: black;">Acta Crystallographica Section D: Biological Crystallography</a> </i> &nbsp;
Ab initio molecular-replacement phasing 189 Figure 1 Schematic of the ab initio molecular-replacement method. Dashed lines indicate optional fine grid searches.  ...  We thank Doug Rees, Paul Adams and Tim Fenn for helpful discussions. Support by the NIH to ATB is gratefully acknowledged (MH63105).  ...  Firstly, all possible models of the inner helical bundle were constructed and used as models in molecular-replacement searches.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s0907444906045793">doi:10.1107/s0907444906045793</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17242512">pmid:17242512</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2483470/">pmcid:PMC2483470</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zjidza6u3nbszmxytdfhyzz5e4">fatcat:zjidza6u3nbszmxytdfhyzz5e4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170812134624/http://journals.iucr.org/d/issues/2007/02/00/sx5064/sx5064.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/e8/0f/e80f36dfcdbef578a16182f03924bff76bac096b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s0907444906045793"> <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/PMC2483470" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Molecular-replacement phasing using predicted protein structures from AWSEM-Suite

Shikai Jin, Mitchell D. Miller, Mingchen Chen, Nicholas P. Schafer, Xingcheng Lin, Xun Chen, George N. Phillips, Peter G. Wolynes
<span title="2020-10-27">2020</span> <i title="International Union of Crystallography (IUCr)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4rhfyrx7xvh4bmdqhfismcwocu" style="color: black;">IUCrJ</a> </i> &nbsp;
When no good solved template exists, predicted structures based partially on templates can sometimes be used to generate models for molecular replacement, thereby extending the lower bound of structural  ...  The key factor in the success of molecular replacement is finding a good template structure.  ...  Metrics for evaluating structure prediction and molecular replacement Three metrics are used to evaluate the accuracy of the structure predictions: r.m.s.d., Qw and GDT-TS.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s2052252520013494">doi:10.1107/s2052252520013494</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uwcxrv5zcvbpjnyeymx4pz7xfa">fatcat:uwcxrv5zcvbpjnyeymx4pz7xfa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201123233236/https://journals.iucr.org/m/issues/2020/06/00/mf5047/mf5047.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/55/ec/55ec0b5ea637014d132d6294235364e420522bf7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s2052252520013494"> <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>

Evaluating the potential of using fold-recognition models for molecular replacement

David T. Jones
<span title="2001-09-21">2001</span> <i title="International Union of Crystallography (IUCr)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6inoqqfovnhtledhw3uuo322xa" style="color: black;">Acta Crystallographica Section D: Biological Crystallography</a> </i> &nbsp;
For molecular-replacement studies, it is common to use not just one model but a set of different models in the search for a phase solution.  ...  Molecular replacement (MR) is a widely used method for bypassing these experimental methods, but here it is necessary for there to be a closely related protein of known three-dimensional structure to act  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s0907444901013403">doi:10.1107/s0907444901013403</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11567156">pmid:11567156</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/inxfekb4wvdfxmxqm4gapxctg4">fatcat:inxfekb4wvdfxmxqm4gapxctg4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808183842/http://journals.iucr.org/d/issues/2001/10/00/ba5016/ba5016.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/e3/32/e3327b12e7a5fa7ad42dc080a1d75e950dd7a45c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s0907444901013403"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts

W. Boomsma, P. Tian, J. Frellsen, J. Ferkinghoff-Borg, T. Hamelryck, K. Lindorff-Larsen, M. Vendruscolo
<span title="2014-09-05">2014</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;
Taken together, these results demonstrate that the molecular fragment replacement strategy can be used in combination with chemical shift information to characterize not only the native structures of proteins  ...  The most widely used approaches adopt the molecular fragment replacement strategy, in which structural fragments are repeatedly reassembled into different complete conformations in molecular simulations  ...  The authors declare no conflict of interest. This article is a PNAS Direct Submission. 1 W.B. and P.T. contributed equally to this work. 2 To whom correspondence may be addressed.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.1404948111">doi:10.1073/pnas.1404948111</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25192938">pmid:25192938</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4183297/">pmcid:PMC4183297</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qusrovmjufhj3gpmupzt72jeru">fatcat:qusrovmjufhj3gpmupzt72jeru</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180723203644/http://www.pnas.org/content/pnas/111/38/13852.full.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/8f/c4/8fc4325b49b82bf64ecaafbeb2c4400df1c66f60.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.1404948111"> <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/PMC4183297" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Assessment of CASP7 predictions in the high accuracy template-based modeling category

Randy J. Read, Gayatri Chavali
<span title="">2007</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;
A new criterion was introduced, the quality of the model for use in solving a crystal structure by molecular replacement.  ...  However, when there is already a good template, few of the models are better for the purpose of molecular replacement. Proteins 2007; 69(Suppl 8):27-37. V V C 2007 Wiley-Liss, Inc.  ...  Quality of models for molecular replacement A large fraction of crystal structures deposited in the PDB is solved using the molecular replacement method.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.21662">doi:10.1002/prot.21662</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17894351">pmid:17894351</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wrwaseescng3vlbffoxpzyxvmm">fatcat:wrwaseescng3vlbffoxpzyxvmm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201106185812/https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/prot.21662" 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/22/41/2241928db08ab01565a89a8541d196183e38f260.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.21662"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Advances inRosettastructure prediction for difficult molecular-replacement problems

Frank DiMaio
<span title="2013-10-12">2013</span> <i title="International Union of Crystallography (IUCr)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6inoqqfovnhtledhw3uuo322xa" style="color: black;">Acta Crystallographica Section D: Biological Crystallography</a> </i> &nbsp;
TheRosettaprotein structure modeling suite can aid in the solution of difficult molecular-replacement problems using templates from 15 to 25% sequence identity;Rosettarefinement guided by noisy density  ...  In this paper, an overview of the use ofRosettafor these difficult molecular-replacement problems is provided and new modeling developments that further improve model quality are described.  ...  ., 2011) has evolved as a comprehensive tool for protein structure modeling, including tools for ab initio structure prediction, protein-protein and protein-ligand docking, loop modeling and structure  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s0907444913023305">doi:10.1107/s0907444913023305</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24189231">pmid:24189231</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3817693/">pmcid:PMC3817693</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/epbsn7ygwvekdm7epsi3wh53zq">fatcat:epbsn7ygwvekdm7epsi3wh53zq</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC3817693/PMC3817693-S0907444913023305.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> File Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ef/cf/efcf588be2104decefb06a914efc582cf2acc977.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s0907444913023305"> <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/PMC3817693" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Molecular replacement: tricks and treats

Chantal Abergel
<span title="2013-10-12">2013</span> <i title="International Union of Crystallography (IUCr)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6inoqqfovnhtledhw3uuo322xa" style="color: black;">Acta Crystallographica Section D: Biological Crystallography</a> </i> &nbsp;
For successful molecular replacement the model must cover at least 50% of the total structure and the Cαr.m.s.d. between the core model and the structure to be solved must be less than 2 Å.  ...  Molecular replacement is the method of choice for X-ray crystallographic structure determination provided that suitable structural homologues are available in the PDB.  ...  We thank Sandra Jeudy, Jean-Michel Claverie and Jorge Navaza for reading the manuscript, as well as the reviewers for their useful remarks. We acknowledge the support of the CNRS, ANR grant No.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s0907444913015291">doi:10.1107/s0907444913015291</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24189227">pmid:24189227</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3817689/">pmcid:PMC3817689</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ryrd2armxrfqhfpn4rgsqnphzi">fatcat:ryrd2armxrfqhfpn4rgsqnphzi</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC3817689/PMC3817689-S0907444913015291.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> File Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/11/e2/11e2f1dc0a60b0612d2e7527aa51199c4f934e69.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s0907444913015291"> <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/PMC3817689" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Validation of the molecular replacement solutions with the OMIT procedure

Y. Vekhter, J. H. Konnert
<span title="2005-08-23">2005</span> <i title="International Union of Crystallography (IUCr)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/w3vqn7pfvvhztgjopipjutfgtq" style="color: black;">Acta Crystallographica Section A Foundations of Crystallography</a> </i> &nbsp;
Konnert, Laboratory for the Structure of Keywords: molecular replacement, model building, ligand P.04.26.29 Acta Cryst. (2005).  ...  E-mail: vekhter@ccs.nrl.navy.mil In the method of molecular replacement, the phases for the initial map of the unknown structure are computed by rotating and translating a trial molecular entity to estimate  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s0108767305088410">doi:10.1107/s0108767305088410</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5oqfj26gr5ea3o7ndia7avvtwe">fatcat:5oqfj26gr5ea3o7ndia7avvtwe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180723133656/http://journals.iucr.org/a/issues/2005/a1/00/a33058/a33058.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/34/c9/34c9ef3a05852b2c78170c998526ae5e0b60061f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s0108767305088410"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

High-Accuracy Protein Structures By Combining Machine-Learning With Physics-Based Refinement [article]

Lim Heo, Michael Feig
<span title="2019-08-10">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
determination via molecular replacement.  ...  The resulting models have highly accurate global and local structure, including high accuracy at functionally important interface residues, and they are highly suitable as initial models for crystal structure  ...  Read for providing scripts for molecular replacement with Phaser. This research was supported by National Institutes of Health Grants R01 GM084953 and R35 GM126948.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/731521">doi:10.1101/731521</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/y6k7qlgaivd73hpimxue24vpyi">fatcat:y6k7qlgaivd73hpimxue24vpyi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200211235318/https://www.biorxiv.org/content/biorxiv/early/2019/08/10/731521.full.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] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/731521"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Initiating heavy-atom-based phasing by multi-dimensional molecular replacement

Bjørn Panyella Pedersen, Pontus Gourdon, Xiangyu Liu, Jesper Lykkegaard Karlsen, Poul Nissen
<span title="2016-03-01">2016</span> <i title="International Union of Crystallography (IUCr)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/b3zks4nhqvgixag6suqb5wlhsu" style="color: black;">Acta Crystallographica Section D: Structural Biology</a> </i> &nbsp;
This is often the case for, for example, membrane proteins. Here, an approach for heavy-atom site identification based on a molecular-replacement parameter matrix (MRPM) is presented.  ...  MRPM is well suited to proteins undergoing large conformational changes where multiple search models should be considered, and it enables the identification of weak but correct molecular-replacement solutions  ...  Andersen for discussions about molecular replacement strategies. We thank Robert M. Stroud and Janet Finer-Moore for reading and reviewing the final manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s2059798315022482">doi:10.1107/s2059798315022482</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26960131">pmid:26960131</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4784675/">pmcid:PMC4784675</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fxgqjkktobcd7lso4idkwmgqwu">fatcat:fxgqjkktobcd7lso4idkwmgqwu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20160309111732/http://journals.iucr.org:80/d/issues/2016/03/00/ba5231/ba5231.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/44/1e/441e95b2048f17bfec85526a35560f32133a5ea0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s2059798315022482"> <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/PMC4784675" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

High-resolution structure prediction and the crystallographic phase problem

Bin Qian, Srivatsan Raman, Rhiju Das, Philip Bradley, Airlie J. McCoy, Randy J. Read, David Baker
<span title="2007-10-14">2007</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/drfdii35rzaibj3aml5uhvr5xm" style="color: black;">Nature</a> </i> &nbsp;
in the absence of templates suitable for molecular replacement from the Protein Data Bank.  ...  The energy-based refinement of low-resolution protein structure models to atomic-level accuracy is a major challenge for computational structural biology.  ...  Acknowledgements We thank Rosetta@home participants for contributing computing power that made testing of many new ideas possible; the DOE INCITE program for access to Blue Gene/L at Argonne National Laboratory  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nature06249">doi:10.1038/nature06249</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17934447">pmid:17934447</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2504711/">pmcid:PMC2504711</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4w6ty7yjqfgpdez6w3f5m3ieve">fatcat:4w6ty7yjqfgpdez6w3f5m3ieve</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20110401074334/http://www.stanford.edu/~rhiju/QianDasRaman_PhaseProblem_Nature2007.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/34/80/3480e588a5a96d64d98c2fa272552121eabc6210.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nature06249"> <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/PMC2504711" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Advances in nucleic acid model building with ARP/wARP 7.6

Grzegorz Chojnowski, Victor Lamzin
<span title="2016-08-28">2016</span> <i title="International Union of Crystallography (IUCr)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rd3cuh2n4rfezc6sy4igtb5jci" style="color: black;">Acta Crystallographica Section A: Foundations and Advances</a> </i> &nbsp;
Our model system is Cdc23 NTerm , a dimeric protein of which the structure has been recently determined via S-SAD at 3.1Å resolution 1 .  ...  The advent of MRSAD has been triggered by the need to reduce the MR intrinsic model bias, in particular at low resolution, and by the increasing availability of high-resolution structures for components  ...  Over the years the ARP/wARP software has been continuously advancing and used by more than 15,000 researchers for building structural models of proteins with or without nucleic acids or small-molecule  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s2053273316096960">doi:10.1107/s2053273316096960</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hpr2bmvkazbkbldrzt64rs4lhe">fatcat:hpr2bmvkazbkbldrzt64rs4lhe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719000649/http://journals.iucr.org/a/issues/2016/a1/00/a54303/a54303.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/4c/76/4c76571d14b21da9a9cafc3b5de16e59096683e2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s2053273316096960"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Molecular Engineering of the Geobacillus stearothermophilus α-Amylase and Cel5E from Chlostridium thermocellim; In Silico Approach

Ibrahim Torktaz, Jafar Hemmat, Ali Asghar Karkhane, Garshasb Rigi, Amin Rostami, Jafar Khezri, Reza Behroozi
<span title="2018-08-01">2018</span> <i title="Definitive International Institute of Life Science (DIILI Publication)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/khkiu3emwnc7nmdpgxkkslhuc4" style="color: black;">Iranian Journal of Biotechnology</a> </i> &nbsp;
Materials and Methods: In this study we predicted the 3D structure of the enzymes, then simulated the molecular docking study using MolDock, PLANTS, and Lamarkian genetic algorithm as scoring functions  ...  for the docking and in silico engineering of the protein aiming to increase the thermal stability and catalytic activity.  ...  Spplementary Data This paper includes a supplementary file containing details of delta G calculation and molecular docking process which is appeared on the web site of the IJB journal (http://www.ijbiotech.com  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.21859/ijb.1284">doi:10.21859/ijb.1284</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sckoez5acvdetpfidzfki3yxru">fatcat:sckoez5acvdetpfidzfki3yxru</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190429051318/http://www.ijbiotech.com/article_64713_f8c5562d8d41e62acc62a9b8f547fd2e.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/6a/ce/6ace784193e5d8ce3bae404564115fa15fbd6b38.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.21859/ijb.1284"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Molecular Engineering of the Geobacillus stearothermophilus α-Amylase and Cel5E from Chlostridium thermocellim; In Silico Approach

Ibrahim Torktaz, Jafar Hemmat, Ali Asghar Karkhane, Garshasb Rigi, Amin Rostami, Jafar Khezri, Reza Behroozi
<span title="2018-08-11">2018</span> <i title="Armenian Green Publishing Co"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/khkiu3emwnc7nmdpgxkkslhuc4" style="color: black;">Iranian Journal of Biotechnology</a> </i> &nbsp;
In this study we predicted the 3D structure of the enzymes, then simulated the molecular docking study using MolDock, PLANTS, and Lamarkian genetic algorithm as scoring functions for the docking and in  ...  Using in silico approach and identifying point mutations in the structure amylase of G. stearothermophilus and Cel5E from C. termocellum we tried to increase thermal stability of the enzymes along with  ...  Spplementary Data This paper includes a supplementary file containing details of delta G calculation and molecular docking process which is appeared on the web site of the IJB journal (http://www.ijbiotech.com  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.15171/ijb.1284">doi:10.15171/ijb.1284</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31457020">pmid:31457020</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6697822/">pmcid:PMC6697822</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rewjdieahvai5olp735lrstxta">fatcat:rewjdieahvai5olp735lrstxta</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200930200311/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6697822&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] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.15171/ijb.1284"> <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/PMC6697822" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Comparison stability Rusticyanin 23270 wild-type and mutant His143Leu using molecular dynamics simulation

R. Jafarpour, F. Fatemi, M. Dehghan Shasaltane
<span title="2022-01-08">2022</span> <i title="SCI AND TECH UNIVERSAL INC"> Journal of Nuclear Research and Applications </i> &nbsp;
The effect of the mutation on the stability of the protein structure was investigated by analysing the results of molecular dynamics simulation on the wild-type and mutant protein.  ...  A suitable template for modeling was prepared from the Swiss model server, and the best protein model was made with Modeller software.  ...  Investigating the effect of mutation on protein structure using molecular dynamics simulation A preliminary study of the His143Leu mutation by server I-Mutant 2.0 shows replacing leucine with histidine  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.24200/jon.2022.1008">doi:10.24200/jon.2022.1008</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fssio7l4sjbk5fqflekfzndksy">fatcat:fssio7l4sjbk5fqflekfzndksy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220112044612/https://jonra.nstri.ir/article_1333_35fe2e1d05c1674d4cf3a5e307b716b7.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/26/99/269919b738876f53581ece545a66cdbb5f9f651f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.24200/jon.2022.1008"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>
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