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Protein structure prediction using a combination of sequence homology and global energy minimization: II. Energy functions

Michael J. Dudek, K. Ramnarayan, Jay W. Ponder
<span title="1998-04-15">1998</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/72zcmi3smndcrdvxgve7ny6ytq" style="color: black;">Journal of Computational Chemistry</a> </i> &nbsp;
A protein energy surface is constructed. Validation is through applications of global energy minimization to surface loops of protein crystal structures.  ...  structures and sublimation energies for nine model compounds; ab initio energies over 1014 conformations of 15 small-molecule dimers; and experimental hydration free energies for 48 model compounds.  ...  homologous protein and from global minimization of a function representing energy.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/(sici)1096-987x(19980415)19:5&lt;548::aid-jcc7&gt;3.0.co;2-m">doi:10.1002/(sici)1096-987x(19980415)19:5&lt;548::aid-jcc7&gt;3.0.co;2-m</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/r6uli3a4vvarbjntpn22ntqysy">fatcat:r6uli3a4vvarbjntpn22ntqysy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20110331182508/http://dasher.wustl.edu/ponder/papers/jcc-19-548-98.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/64/2c/642cc4cbf4fc9cebd2e378cd35ef1a81cca72e6f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/(sici)1096-987x(19980415)19:5&lt;548::aid-jcc7&gt;3.0.co;2-m"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Knowledge based structure prediction of the light-harvesting complex II of rhodospirillum molischianum [chapter]

Xiche Hu, Dong Xu, Kenneth Hamer, Klaus Schulten, Juergen Koepke, Hartmut Michel
<span title="1995-11-15">1995</span> <i title="American Mathematical Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/vvrs4aeb5fbclnb6drlj6n6v5i" style="color: black;">Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding</a> </i> &nbsp;
We illustrate in this article how one proceeds to predict the structure of integral membrane proteins using a combined approach in which molecular dynamics simulations and energy minimization are performed  ...  A consensus assignment for secondary structure was derived from a combination of all the prediction methods used.  ...  We illustrate in this article how one proceeds to predict the structure of integral membrane proteins using a combined approach in which molecular dynamics simulations and energy minimization are performed  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1090/dimacs/023/07">doi:10.1090/dimacs/023/07</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/dimacs/HuXHSKM95.html">dblp:conf/dimacs/HuXHSKM95</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7qxqflozxrdtbggotapiv3jfny">fatcat:7qxqflozxrdtbggotapiv3jfny</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20040124233842/http://www.ks.uiuc.edu:80/Publications/Papers/PDF/HU96/HU96.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/bd/ea/bdeaae2b0e792643cb0e3acc3c4f5718a4c572f9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1090/dimacs/023/07"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Near-native structure refinement using in vacuo energy minimization

C. M. Summa, M. Levitt
<span title="2007-02-20">2007</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;
We use a powerfully convergent energy-minimization method and show that, of the traditional molecular mechanics potentials tested, only one showed a modest net improvement over a large data set of structurally  ...  Minimization from the native structure is a weak test of potential energy functions: It is complemented by a much stronger test in which the same methods are compared for their ability to attract a near-native  ...  We thank Erik Lindahl (GROMACS) for modifying GROMACS to use the ENCAD energy function; Ram Samudrala (RAMP and residuespecific all-atom conditional probability discriminatory function) and Erik Sorin  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.0611593104">doi:10.1073/pnas.0611593104</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17360625">pmid:17360625</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1802011/">pmcid:PMC1802011</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/koptizjzxngiphjxzafqpottve">fatcat:koptizjzxngiphjxzafqpottve</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809062924/http://www.cs.uno.edu/~csumma/docs/Summa_and_Levitt_PNAS_2007.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/1a/f2/1af27c92364dbb2c33abd03150d2e043aa008d8e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.0611593104"> <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/PMC1802011" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

3Drefine: Consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization

Debswapna Bhattacharya, Jianlin Cheng
<span title="2012-09-26">2012</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;
The first step is based on optimization of hydrogen bonding (HB) network and the second step applies atomic-level energy minimization on the optimized model using a composite physics and knowledge-based  ...  One of the major limitations of computational protein structure prediction is the deviation of predicted models from their experimentally derived true, native structures.  ...  Acknowledgments The authors thank the anonymous reviewers for a very careful review. Work partially supported by a NIH grant (R01GM093123) to JC.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.24167">doi:10.1002/prot.24167</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22927229">pmid:22927229</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3634918/">pmcid:PMC3634918</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zbhldbwbnzggvgdk3k442nusqy">fatcat:zbhldbwbnzggvgdk3k442nusqy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200206070623/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3634918&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/21/f0/21f0789be6894acf0f28007a847910a776c76768.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.24167"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634918" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

FOLD HELICAL PROTEINS BY ENERGY MINIMIZATION IN DIHEDRAL SPACE AND A DFIRE-BASED STATISTICAL ENERGY FUNCTION

HONGZHI LI, YAOQI ZHOU
<span title="">2005</span> <i title="World Scientific Pub Co Pte Lt"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zudjdcas3bcm3lfnfxnjyl5zty" style="color: black;">Journal of Bioinformatics and Computational Biology</a> </i> &nbsp;
The energy function was used to minimize 2000 random initial structures of 41 small and medium-sized helical proteins in a dihedral space with a fixed helical region.  ...  The energy function (together with a simple clustering of similar structures) also makes a reasonable selection of near-native structures from minimized structures.  ...  Z. is also partially supported by a two-base grant from the National Science Foundation of China.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/s0219720005001430">doi:10.1142/s0219720005001430</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16278952">pmid:16278952</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/e7k2lmu73fhn3ptldu4y7kaskm">fatcat:e7k2lmu73fhn3ptldu4y7kaskm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190227120824/http://pdfs.semanticscholar.org/8005/790c3822b5a7e7f54a3dc65b745f35267e50.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/80/05/8005790c3822b5a7e7f54a3dc65b745f35267e50.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/s0219720005001430"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> worldscientific.com </button> </a>

Investigating the unknown functions in the minimal bacterial genome reveals many transporter proteins [article]

Magdalena Antczak, Martin Michaelis, Mark Wass
<span title="2018-07-31">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Application of state of the art in silico methods for functional annotation demonstrated that these proteins of unknown function lack orthologs, known protein domains, and templates to model their structure  ...  Combination of the results from different complementary approaches enabled functions to be assigned to 94 of the 149 proteins, although often with general terms such as transporter or DNA binding. 22 likely  ...  Stefano Toppo for advice regarding transformation of Argot2.5 scores into probabilities.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/381657">doi:10.1101/381657</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/r6y4nswrzzhx3mri2h5pv4hw74">fatcat:r6y4nswrzzhx3mri2h5pv4hw74</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190429101043/https://www.biorxiv.org/content/biorxiv/early/2018/07/31/381657.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/22/a6/22a688330cdfc30c7e7c0cd9bdd769997dcb5734.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/381657"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Top-down free-energy minimization on protein potential energy landscapes

B. W. Church, D. Shalloway
<span title="2001-05-08">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;
Using the computational folding of a ␤-hairpinforming peptide as an example, we show that such predictive properties indeed exist and can be used for structure prediction by free-energy global minimization  ...  N ew methods have been developed in recent years for using the global properties of protein potential energy landscapes to analyze overall thermodynamic and kinetic properties of protein ensembles.  ...  Berry for a critical review of the manuscript, R. Elber, J. Straub, D. Thirumalai, and P.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.101030498">doi:10.1073/pnas.101030498</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11344256">pmid:11344256</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC33428/">pmcid:PMC33428</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fjbfjilzpfcqfpulsxqj2vmv2m">fatcat:fjbfjilzpfcqfpulsxqj2vmv2m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180729185857/http://www.pnas.org/content/pnas/98/11/6098.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/a4/de/a4de6ac802828ecbc0823a7c1b93ada3aaebadb6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.101030498"> <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/PMC33428" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Structural proteomics of minimal organisms: conservation of protein fold usage and evolutionary implications

John-Marc Chandonia, Sung-Hou Kim
<span title="2006-03-28">2006</span> <i title="Springer (Biomed Central Ltd.)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/m36qvjwuvnegpgzopqbhvg7k3e" style="color: black;">BMC Structural Biology</a> </i> &nbsp;
We analyze the structures of these proteins as they relate to cellular functions, and compare conservation of fold usage between functional categories.  ...  Determining the complete repertoire of protein structures for all soluble, globular proteins in a single organism has been one of the major goals of several structural genomics projects in recent years  ...  Acknowledgements This work is supported by grants from the NIH (1-P50-GM62412) and the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1472-6807-6-7">doi:10.1186/1472-6807-6-7</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16566839">pmid:16566839</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1488858/">pmcid:PMC1488858</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fgdezgxsvvf35iqfgfa6ba6fmm">fatcat:fgdezgxsvvf35iqfgfa6ba6fmm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190428125821/https://bmcstructbiol.biomedcentral.com/track/pdf/10.1186/1472-6807-6-7" 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/38/91/38910af16eec52b45c3d5456bb117fa422fe4e67.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1472-6807-6-7"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1488858" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra

Thomas Evangelidis, Santrupti Nerli, Jiří Nováček, Andrew E. Brereton, P. Andrew Karplus, Rochelle R. Dotas, Vincenzo Venditti, Nikolaos G. Sgourakis, Konstantinos Tripsianes
<span title="2018-01-26">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a4wan6l5o5dfzn767kyz7jqevi" style="color: black;">Nature Communications</a> </i> &nbsp;
Our results on four targets ranging in size from 15.5 to 27.3 kDa illustrate that the structures of proteins can be determined accurately and in an unsupervised manner in a matter of days.  ...  Our results on four targets ranging in size from 15.5 to 27.3 kDa illustrate that the structures of proteins can be determined accurately and in an unsupervised manner in a matter of days.  ...  II, and a Marie Curie Career Integration Grant (618223) to K.T., by NIH grant R01GM083136 to P.A.K., a K-22 Career Development and an R35 Outstanding Investigator Award to N.G.S. through NIAID(AI2573-  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-017-02592-z">doi:10.1038/s41467-017-02592-z</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29374165">pmid:29374165</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5786013/">pmcid:PMC5786013</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3gof7uol7fev5em3rhdbo26wom">fatcat:3gof7uol7fev5em3rhdbo26wom</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501100241/https://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=2075&amp;context=chem_pubs" 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/59/b4/59b42147e574b2f4fdd7ffba1210243710b3ec3c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-017-02592-z"> <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/PMC5786013" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Minimal tool set for a prokaryotic circadian clock

Nicolas M. Schmelling, Robert Lehmann, Paushali Chaudhury, Christian Beck, Sonja-Verena Albers, Ilka M. Axmann, Anika Wiegard
<span title="2017-07-21">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/frh6t5i3jveazlshhan2ekhgcq" style="color: black;">BMC Evolutionary Biology</a> </i> &nbsp;
However, interaction and function of non-cyanobacterial Kai-proteins as well as homologous input and output components remain mainly unclear.  ...  Further, we studied KaiC sequence conservation to determine functionally important regions of diverged KaiC homologs.  ...  Two very recent studies provide a structural basis for the dynamic assembly of clock proteins by using crystallography and NMR [32] , and mass spectrometry and cryo-electron microscopy of the native proteins  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12862-017-0999-7">doi:10.1186/s12862-017-0999-7</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28732467">pmid:28732467</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5520375/">pmcid:PMC5520375</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mdwbbsf2kffzldmnewnyggj63e">fatcat:mdwbbsf2kffzldmnewnyggj63e</a> </span>
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Diversification of methanogens into hyperalkaline serpentinizing environments through adaptations to minimize oxidant limitation

Elizabeth M. Fones, Daniel R. Colman, Emily A. Kraus, Ramunas Stepanauskas, Alexis S. Templeton, John R. Spear, Eric S. Boyd
<span title="2020-11-30">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ii4mp46mlndibnz4acpdnnmvou" style="color: black;">The ISME Journal</a> </i> &nbsp;
Surprisingly, Type II, which branched from the Type I lineage, lacked homologs of two key oxidative [NiFe]-hydrogenases.  ...  These functions were presumably replaced by formate dehydrogenases that oxidize formate to yield reductant and cytoplasmic CO2 via a pathway that was unique among characterized Methanobacteria, allowing  ...  Acknowledgements This work was supported by a grant from the NASA Astrobiology Institute (NNA15BB02A) to JRS, AST, and ESB, and by NSF grants OCE-1335810 and OIA-1826734 to RS.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41396-020-00838-1">doi:10.1038/s41396-020-00838-1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33257813">pmid:33257813</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uf7gwmt2ufbzvgu5g5fwgjyqwm">fatcat:uf7gwmt2ufbzvgu5g5fwgjyqwm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210429005151/https://www.nature.com/articles/s41396-020-00838-1.pdf?error=cookies_not_supported&amp;code=203c01e6-0d55-4e48-a4e9-94722f0abb42" 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/3f/7d3fed334435840455feabb0955480c6874cb3a2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41396-020-00838-1"> <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>

Steiner minimal trees, twist angles, and the protein folding problem

J. MacGregor Smith, Yunho Jang, Moon K. Kim
<span title="2006-12-15">2006</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;
The q value is shown to be inversely proportional to the torsion energy. Hence, it should be a useful approximation to the potential energy function.  ...  Finally, the Steiner ratio is used to evaluate folded and misfolded protein structures.  ...  This inverse relationship then affords a useful alternative measure of the energy function in proteins. The Steiner ratio becomes a surrogate for measuring energy in the protein structure.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.21257">doi:10.1002/prot.21257</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17173288">pmid:17173288</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pxg6wmarqjbphiumxmwnrxbn3i">fatcat:pxg6wmarqjbphiumxmwnrxbn3i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20120603061315/http://www.ecs.umass.edu/mie/faculty/smith/proteins_march2007.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/d4/89d4fe48ef057a7b3517dbcf4ad94e364f0dee89.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.21257"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Multiple Origins and Specific Evolution of CRISPR/Cas9 Systems in Minimal Bacteria (Mollicutes)

Thomas Ipoutcha, Iason Tsarmpopoulos, Vincent Talenton, Christine Gaspin, Annick Moisan, Caray A. Walker, Joe Brownlie, Alain Blanchard, Patricia Thebault, Pascal Sirand-Pugnet
<span title="2019-11-21">2019</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/67anf6qgandy5adz4rakospiuq" style="color: black;">Frontiers in Microbiology</a> </i> &nbsp;
A global survey was conducted to identify and compare CRISPR/Cas systems found in the genome of these minimal bacteria.  ...  Structure of the predicted crRNA/tracrRNA hybrids was conserved and showed typical stem-loop structures pairing the Direct Repeat part of crRNAs with the 5' region of tracrRNAs.  ...  AUTHOR CONTRIBUTIONS TI and PS-P designed the study. TI, IT, VT, CG, AM, CW, PT, and PS-P performed the analyses and analyzed the data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fmicb.2019.02701">doi:10.3389/fmicb.2019.02701</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31824468">pmid:31824468</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6882279/">pmcid:PMC6882279</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yzi3bkrtcvdbjbfkx5ilnctuhu">fatcat:yzi3bkrtcvdbjbfkx5ilnctuhu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191129143301/https://fjfsdata01prod.blob.core.windows.net/articles/files/500765/pubmed-zip/.versions/1/.package-entries/fmicb-10-02701/fmicb-10-02701.pdf?sv=2015-12-11&amp;sr=b&amp;sig=wAbGI0s%2FB7Xz1af1LOjlWkOytmR%2Bkae99igk3zEoztM%3D&amp;se=2019-11-29T14%3A33%3A30Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fmicb-10-02701.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/8d/72/8d7236e378973928d085b2f35a8d6d8bd782bd65.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fmicb.2019.02701"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6882279" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Dynamics of the minimally frustrated helices determine the hierarchical folding of small helical proteins

M. Compiani, E. Capriotti, R. Casadio
<span title="2004-05-12">2004</span> <i title="American Physical Society (APS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nuk2stxzvvhf7ljciu325kj77m" style="color: black;">Physical Review E</a> </i> &nbsp;
We show that a neural network devised to predict native secondary structures from sequence can be used to estimate the probabilities of formation of these helical traits as they are embedded in the protein  ...  This stresses that the minimally frustrated helices of these helical proteins comprise the minimal set of determinants of the folding process.  ...  and Homologous and Heterologous Expression" and "Development and implementation of algorithms for predicting protein structure."  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1103/physreve.69.051905">doi:10.1103/physreve.69.051905</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15244845">pmid:15244845</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cx2ec3p5zbdhdnvikvkbhge36e">fatcat:cx2ec3p5zbdhdnvikvkbhge36e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170301142621/http://biofold.org/pages/documents/papers/PysRevE.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/2b/5f/2b5fa5d10625bb7e6008b731c72f18cbfa8b39f1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1103/physreve.69.051905"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> aps.org </button> </a>

Improving the Physical Realism and Structural Accuracy of Protein Models by a Two-Step Atomic-Level Energy Minimization

Dong Xu, Yang Zhang
<span title="">2011</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
To address this issue, we developed a new program, called ModRefiner, to construct and refine protein structures from Ca traces based on a two-step, atomic-level energy minimization.  ...  Most protein structural prediction algorithms assemble structures as reduced models that represent amino acids by a reduced number of atoms to speed up the conformational search.  ...  Our data demonstrate that ModRefiner can become a useful and convenient program in the field of protein structure prediction.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2011.10.024">doi:10.1016/j.bpj.2011.10.024</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22098752">pmid:22098752</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3218324/">pmcid:PMC3218324</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ywudvyewpjhz3itiowzderxv6y">fatcat:ywudvyewpjhz3itiowzderxv6y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20120714000344/http://zhanglab.ccmb.med.umich.edu/papers/2011_11.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/e6/17/e617bbd45867a0b6dc24ef6d679c3945fff8bb06.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2011.10.024"> <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/PMC3218324" 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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