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LoopIng: a template-based tool for predicting the structure of protein loops

Mario Abdel Messih, Rosalba Lepore, Anna Tramontano
<span title="2015-08-06">2015</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Results: We describe a method, LoopIng, based on the Random Forest automated learning technique, which, given a target loop, selects a structural template for it from a database of loop candidates.  ...  The method returns a confidence score for the predicted template loops and has the advantage of being very fast (on average: 1 min/loop).  ...  Acknowledgements The authors are grateful to all other members of the Biocomputing Unit for their valuable feedbacks and useful discussions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btv438">doi:10.1093/bioinformatics/btv438</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26249814">pmid:26249814</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4653384/">pmcid:PMC4653384</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/p6db45wnnfg6jemdclux4wywxa">fatcat:p6db45wnnfg6jemdclux4wywxa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190428054537/https://iris.uniroma1.it/retrieve/handle/11573/862539/213057/Messih_LoopIng_2015.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/af/43/af43c3335886c29a321142b06d833435815086fd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btv438"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4653384" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

DaReUS-Loop: a web server to model multiple loops in homology models

<span title="2019-07-02">2019</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
It also provides a prediction confidence level that corresponds to the expected accuracy of the loops.  ...  Here, a DaReUS-Loop web server is presented, providing an automated platform for modeling or remodeling loops in the context of homology models.  ...  Template based docking provides a prediction of an entire protein-protein complex as a lowresolution model that needs to be refined (48) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkz403">doi:10.1093/nar/gkz403</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31114872">pmid:31114872</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6602439/">pmcid:PMC6602439</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mpezolvbdfcknpepih623x6pbi">fatcat:mpezolvbdfcknpepih623x6pbi</a> </span>
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A fold-recognition approach to loop modeling

Christer Levefelt, Dan Lundh
<span title="2005-11-08">2005</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/45p53qd7nrhxteu6rfvh5pcqay" style="color: black;">Journal of Molecular Modeling</a> </i> &nbsp;
Comparative or homology modeling [3] predicts structure primarily based on similarity between the sequence of the target protein and those of one or more template proteins of known structure.  ...  A novel approach is proposed for modeling of loop regions in proteins.  ...  Many methods for prediction of protein structure align the target amino acid sequence to a structural template derived from a known protein.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00894-005-0003-0">doi:10.1007/s00894-005-0003-0</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16096805">pmid:16096805</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hvylkykiwjgw3ce264vpy27sie">fatcat:hvylkykiwjgw3ce264vpy27sie</a> </span>
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Sequence–structure relationships in RNA loops: establishing the basis for loop homology modeling

Christian Schudoma, Patrick May, Viktoria Nikiforova, Dirk Walther
<span title="2009-11-18">2009</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
We established a threshold that may guide the sequence divergence-based selection of template structures for RNA loop homology modeling.  ...  RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts.  ...  ACKNOWLEDGEMENTS Molecular graphics images were produced using the UCSF Chimera package (38) from the Resource for Biocomputing, Visualization and Informatics at the University of California, San Francisco  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkp1010">doi:10.1093/nar/gkp1010</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19923230">pmid:19923230</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2817452/">pmcid:PMC2817452</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6r5vx2lyhrdc7dnkzqoxzrkz5q">fatcat:6r5vx2lyhrdc7dnkzqoxzrkz5q</a> </span>
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RCD+: Fast loop modeling server

José Ramón López-Blanco, Alejandro Jesús Canosa-Valls, Yaohang Li, Pablo Chacón
<span title="2016-05-05">2016</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Modeling loops is a critical and challenging step in protein modeling and prediction.  ...  Sample results page provided by the server for a bacterial hydrolase loop (PDB-ID 1qwl).  ...  Ab initio methods build feasible loop conformations from scratch whereas template-based methods locate a best fit from a structural library of loops extracted from the Protein Data Bank (PDB).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkw395">doi:10.1093/nar/gkw395</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27151199">pmid:27151199</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4987936/">pmcid:PMC4987936</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jt7vjsvba5f53iahrcnyayasuq">fatcat:jt7vjsvba5f53iahrcnyayasuq</a> </span>
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Modeling of loops in proteins: a multi-method approach

Michal Jamroz, Andrzej Kolinski
<span title="">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/m36qvjwuvnegpgzopqbhvg7k3e" style="color: black;">BMC Structural Biology</a> </i> &nbsp;
Results: For a representative set of protein structures of various structural classes test predictions of loop regions have been performed using MODELLER, ROSETTA, and a CABS coarse-grained de novo modeling  ...  Loops of various length, from 4 to 25 residues, were modeled assuming an ideal target-template alignment of the remaining portions of the protein.  ...  A commercial version of CABS-based modeling software was used http://www.selvita.com/selvita-protein-modeling-platform. html.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1472-6807-10-5">doi:10.1186/1472-6807-10-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20149252">pmid:20149252</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2837870/">pmcid:PMC2837870</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kafh46yg2rfxnoglxey75jnaem">fatcat:kafh46yg2rfxnoglxey75jnaem</a> </span>
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R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops

Piroon Jenjaroenpun, Thidathip Wongsurawat, Sawannee Sutheeworapong, Vladimir A. Kuznetsov
<span title="2016-11-28">2016</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
R-loopDB (http://rloop.bii.a-star.edu.sg) was originally constructed as a collection of computationally predicted R-loop forming sequences (RLFSs) in the human genic regions.  ...  It includes genome-scale prediction of RLFSs for humans, six other animals and yeast.  ...  ACKNOWLEDGEMENTS The authors thank Tan Xuanru Mavis for the discussion and data processing.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkw1054">doi:10.1093/nar/gkw1054</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27899586">pmid:27899586</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5210542/">pmcid:PMC5210542</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/aiirjzchsvbexnwknnfelr7xbu">fatcat:aiirjzchsvbexnwknnfelr7xbu</a> </span>
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High-Throughput Single-Molecule R-loop Footprinting Reveals Principles of R-loop Formation [article]

Maika Malig, Stella R Hartono, Jenna M Giafaglione, Lionel A Sanz, Frederic Chedin
<span title="2019-05-17">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
R-loops are a prevalent class of non-B DNA structures that form during transcription upon reannealing of the nascent RNA to the template DNA strand.  ...  Non-denaturing sodium bisulfite treatment catalyzes the conversion of unpaired cytosines to uracils, creating permanent genetic tags for the position of an R-loop.  ...  Acknowledgments We thank members of the Chedin lab for critical feedback and useful discussions. We also thank Tonia Brown for editing this work.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/640094">doi:10.1101/640094</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gjhbqf4d3fapxpbn44js5o5zne">fatcat:gjhbqf4d3fapxpbn44js5o5zne</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200212004558/https://www.biorxiv.org/content/biorxiv/early/2019/05/17/640094.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/10.1101/640094"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Identification and immunogenic properties of recombinant ZnuD protein loops of Acinetobacter baumannii

Maryam Mobarak Qamsari, Iraj Rasooli, Shakiba Darvish Alipour Astaneh
<span title="">2020</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/vusydvbzgfck3ik2qu2c5h4zea" style="color: black;">Informatics in Medicine Unlocked</a> </i> &nbsp;
Conclusion: The results indicated that ZnuD and most of its antigenic loops are potentially suitable antigens for subunit vaccine development approaches.  ...  They have a critical role in A.baumannii physiology and pathogenicity as a cofactor of many enzymes and DNAbinding proteins.  ...  Ethical Statement The manuscript entitled: "Identification and immunogenic properties of recombinant ZnuD protein loops of Acinetobacter baumannii", is submitted for publication in "Informatics in Medicine  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.imu.2020.100342">doi:10.1016/j.imu.2020.100342</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zlvhhd5imncxnnrtqu3643xx2y">fatcat:zlvhhd5imncxnnrtqu3643xx2y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200512082640/https://pdf.sciencedirectassets.com/312075/AIP/1-s2.0-S2352914820300526/main.pdf?X-Amz-Security-Token=IQoJb3JpZ2luX2VjEPj%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLWVhc3QtMSJHMEUCID1JK6Jm01sh7UswKqm8boQwoVV2O85A%2FKfepZPx2wVqAiEAtDw6pAOfN5FJO8Zhl1nuSVX3sJk8YUnMsJ04KHecV0MqtAMIQBADGgwwNTkwMDM1NDY4NjUiDByYPCkX%2BtNbY61xsiqRA3G0F152%2BV3WeaAZjC82AnE%2BAxgNun%2BSvcL6ETAxs14EO3W8OnuiLC%2FhU0fX9%2FLsVDdPegFV4C7y8BC0MGNu1NF%2BkzjQwkw4Ng7lLE6cjAfw6CKQAz5RRb9oyBapPQxcYoIIx2OvGR4r%2FEOl3q4vkz1l%2BriDaSu%2BIL3XY1Wfn%2Bdy3FoTJXGMvlCNmibXqtE8o%2BspxFctMAA6DFF5PsMClLWfCufnEF7XUA0HsaosuXyXwVU9OzIH6Oc0OyRN2mVYPDrxmx5mTYAiTChNMl3UUo7QOLtw8f2gQo%2FEwmrVBdwbuPH2p4nnXGiegrnHPdrCYL1ZJLVYYxPRAiMlnIfJKU5yXqu00E9jYdG4YHaqOr1d%2Bbex9FueS0q6r3f7bqN3gSqC9P9YfI0ZvRLIWDfPHfkvh3KVkx2y6rE4tGCgcIHIYvXVC3UkRK0vpaWgHZ7T6KJ5w91DaVJxQ%2B39rwj32qZRS7X9keLHqR6mm6H0sSHsyo2qxe1AiIfMxAFuAxSFWBuOGBKbvcWlAeBtyiVQDY00MN%2Bb6fUFOusBRtKCgWt%2F7YeN80cICfmhfQcdkutmCjk51pM46x%2FBKasqdcUC3rN%2BDJR797fG8ib5yWwX1OlMO4M4LBMrUKwNeCrakHpiMzHxJs5rLSSlbJAvXVYROcC3zZp1Cfhui3plXA%2FyiD%2FUK3q3Hoj%2BXiaiLauYBckpQnK7kqAv26G33xkOm0utMg0oG%2BVlWN7n44ttNZc9iIcSTiVGk7C6Z2I3dcOc%2Fi5NTh31YC9gX3Mh7wP5GLPZfw1QN%2F8s47YzjvSXBoD626bLnxudIS7VsmFoGKTQLlL6zcEJZmeUANOJMax5MUtybzzOAd6XEQ%3D%3D&amp;X-Amz-Algorithm=AWS4-HMAC-SHA256&amp;X-Amz-Date=20200512T082634Z&amp;X-Amz-SignedHeaders=host&amp;X-Amz-Expires=300&amp;X-Amz-Credential=ASIAQ3PHCVTYT6EPQAUH%2F20200512%2Fus-east-1%2Fs3%2Faws4_request&amp;X-Amz-Signature=66e305f05f15c08de827d32b91e05b7945c5bb3c7686a0c42922d321f0cb2eed&amp;hash=69be41ed91e00504ea87f27ad704f4d807eda1dba544e2acf642627bcf41b0e0&amp;host=68042c943591013ac2b2430a89b270f6af2c76d8dfd086a07176afe7c76c2c61&amp;pii=S2352914820300526&amp;tid=spdf-af0c62c7-a764-43d4-aca6-03f2859971b5&amp;sid=5cf5022e43d9e149fd982139aa1effe0e3a8gxrqa&amp;type=client" 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/6c/db6cab0d691ea14463f1584dffd48a875cdd175f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.imu.2020.100342"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a>

Current approaches to flexible loop modeling

Amélie Barozet, Pablo Chacón, Juan Cortés
<span title="">2021</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/f3yvu6my5fd5vcuhudofh4mh6u" style="color: black;">Current Research in Structural Biology</a> </i> &nbsp;
., Current approaches to flexible loop modeling, Current Research in Structural Biology (2021), doi: https://doi.  ...  Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper  ...  Acknowledgments This work has been supported by the French National Research Agency (ANR) through grant ANR-19-PI3A-0004 and by the Spanish grants BFU2016-76220-P and PID2019-109041GB-C21 (AEI,10.13039  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.crstbi.2021.07.002">doi:10.1016/j.crstbi.2021.07.002</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nvqhvfzj6bea3h4u2probkc3ua">fatcat:nvqhvfzj6bea3h4u2probkc3ua</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210806130509/https://pdf.sciencedirectassets.com/321102/AIP/1-s2.0-S2665928X21000143/main.pdf?X-Amz-Security-Token=IQoJb3JpZ2luX2VjEEQaCXVzLWVhc3QtMSJIMEYCIQCmqj37DQc30rY3axzXSp3sZLptrFExSLgL4%2BZO0hZp5AIhAIQ9R%2BimTmuFLDmUaAF0Ej1N5ouNCii42hJVEcaSyPsoKvoDCF0QBBoMMDU5MDAzNTQ2ODY1IgyS7Les4uhIpTDOxN8q1wPKld2ZpRB%2FXI2wuTUShJS6O8uLlKed959bAbOS6xyhLgIxRUURC5VB4eL73vjNB5pLQfTwZNmd5Gp6gzYDEsxNybGNDjLrsLovjp4BaxOlxElJU4%2BWr%2BVDbUEDDK5PVvr4QUTetKL4vnagXwT9AwWid%2F7cnPeHjdgCmPPa%2FDeIB5V%2FdYMw4KtGD1scp0gUtnsi5Ls073Z1uE9D7Nk%2Fx%2F%2BbZpgrT7iX5evk%2FiIybecgBOI%2B1maGZX6G6OZy8EaErigcB0n56UqLP4pSAR%2FCqMuWohWRt7YzsL0ab60eloOA9yLqCPOBChV4jwFBWSzpedssfrr1ZWjlA8r%2BwSHj9GBz3CDKZX8b4Oww4VyrXrdqTJ%2Fuwv1N1IrSkVjXF9L5e1Sx4ZUbbAeSpF6NZv1MRssqpijv2RyucEU5VesVps7hIJFwxL1q1tgJo3B%2BNNg%2FEKlyMsLTCY4F1Ia%2ByMMMGvybtjwGljgKsy41UP9trUh1JeT54cy35qaWMSMQxAdfndsk%2FYfDTjkZiTXmpsDzDj8l%2Bd6fON001HgZo5aHvDzWISKgoI9jYjST%2B6g%2BtookObp5KJAE7Hg2%2F6FoAXx7%2BwZYdOY6ZfeWsUXxpZX6p7315OtF%2B1xmJVww5MS0iAY6pAHRFJDZiYsY5wS4QxZhCU%2BHskyYzjHFxdeD0NDqBGJ1NKZBPKm5lX9pe09KGDm5EDkcUoExaaxxqsRDyAufKMAzPSIyB8qM%2FkZ8ohjVH3wQxyDy4UxEq0j5tzWfjzwFJkFSKzx37SYHqL88Bq1Apagf5sGQhkvSkWRNfb5fonuw%2FmEtPbXdLgnuLymoo5ddHETS0%2Bx160RIRHT2QCkjwLr2kYqFbg%3D%3D&amp;X-Amz-Algorithm=AWS4-HMAC-SHA256&amp;X-Amz-Date=20210806T130504Z&amp;X-Amz-SignedHeaders=host&amp;X-Amz-Expires=300&amp;X-Amz-Credential=ASIAQ3PHCVTY7CNASNUN%2F20210806%2Fus-east-1%2Fs3%2Faws4_request&amp;X-Amz-Signature=b56e439e1bc02f9557be033daa0a4e6dc1c9a955196e748ae85f6fe0226b2585&amp;hash=da48afe390c1b6fb1e22226f58545d9a296c1c089e7aa4bbfdde3041010675e6&amp;host=68042c943591013ac2b2430a89b270f6af2c76d8dfd086a07176afe7c76c2c61&amp;pii=S2665928X21000143&amp;tid=spdf-3ea17faf-d9bf-4665-a3d1-f027ce92c2df&amp;sid=f645b4127a913044b308503656e3995351fcgxrqa&amp;type=client" 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/ff/c9/ffc992f4778cd27d9f6ffcf804a233428c93483e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.crstbi.2021.07.002"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a>

CONFORMATIONAL SAMPLING IN TEMPLATE-FREE PROTEIN LOOP STRUCTURE MODELING: AN OVERVIEW

Yaohang Li
<span title="">2013</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cmflnsn2l5gylcviv447te3mku" style="color: black;">Computational and Structural Biotechnology Journal</a> </i> &nbsp;
Distribution of loop lengths in the protein chain list generated by the PISCES server [21] on Aug. 28, 2012 containing 13255 chains with 2.0A resolution, 90% sequence identity, and 0.25 R-factor cutoff  ...  The template-based methods [22] [23] [24] [25] search PDB for loop structure templates that fit the geometric and topologic constraints of the loop stems.  ...  As a result, accurate prediction of the loop regions conformations in proteins is important for a variety of structural biology applications, including determining the surface loop regions in comparative  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5936/csbj.201302003">doi:10.5936/csbj.201302003</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24688696">pmid:24688696</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3962101/">pmcid:PMC3962101</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ho5hi4opwzck5pmza5s2pxbooy">fatcat:ho5hi4opwzck5pmza5s2pxbooy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190323044709/https://core.ac.uk/download/pdf/82804272.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/6d/7b/6d7b223861a7a5574c04618c15fcaad221231f34.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5936/csbj.201302003"> <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/PMC3962101" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

COMPREHENSIVE ANALYSIS OF SEQUENCE-STRUCTURE RELATIONSHIPS IN THE LOOP REGIONS OF PROTEINS

SHUGO NAKAMURA, KENTARO SHIMIZU
<span title="">2009</span> <i title="PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO."> Genome Informatics 2009 </i> &nbsp;
Local sequence-structure relationships in the loop regions of proteins were comprehensively estimated using simple prediction tools based on support vector regression (SVR).  ...  on the mechanism of protein folding and prediction of the tertiary structure of proteins without using structural templates.  ...  Most of the local structure prediction tools that were recently proposed are based on the prediction of a sequence of structural alphabets.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/9781848165632_0010">doi:10.1142/9781848165632_0010</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ffin6zl2orh6thorltjfrgr7la">fatcat:ffin6zl2orh6thorltjfrgr7la</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171026003150/https://core.ac.uk/download/pdf/22875659.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/f3/be/f3bea34b9d8fbf387b50e1b54288252a3219469a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/9781848165632_0010"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> worldscientific.com </button> </a>

RNA loop–loop interactions as dynamic functional motifs

Christine Brunel, Roland Marquet, Pascale Romby, Chantal Ehresmann
<span title="">2002</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lghpknjtojbgplyc2rshxw5ofm" style="color: black;">Biochimie</a> </i> &nbsp;
The fate of the initial reversible loop-loop complex is dictated by both functional and structural constraints.  ...  The second one concerns the dimerization of HIV-1 genomic RNA, which is responsible for the encapsidation of a diploid RNA genome.  ...  Acknowledgements We wish to thank all the members of the laboratory who have contributed or/and still contribute to the work described in this review, as well as members of other laboratories who provided  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0300-9084(02)01401-3">doi:10.1016/s0300-9084(02)01401-3</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12458085">pmid:12458085</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/oxns4v2anrgszimvkpri5geecy">fatcat:oxns4v2anrgszimvkpri5geecy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20041126150638/http://www2.ee.ntu.edu.tw:80/~b9901059/Biochi925.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/ca/44cada2af3d06b552dee09d7854ac94f0b96e33a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0300-9084(02)01401-3"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Comprehensive analysis of sequence-structure relationships in the loop regions of proteins

Shugo Nakamura, Kentaro Shimizu
<span title="">2009</span> <i title="Universal Academy Press Inc"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jf2bmhtlzjh4zjrkh3rivxd2sq" style="color: black;">Genome Informatics Series</a> </i> &nbsp;
Local sequence-structure relationships in the loop regions of proteins were comprehensively estimated using simple prediction tools based on support vector regression (SVR).  ...  on the mechanism of protein folding and prediction of the tertiary structure of proteins without using structural templates.  ...  Most of the local structure prediction tools that were recently proposed are based on the prediction of a sequence of structural alphabets.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20180266">pmid:20180266</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nejow4bs3zboraiyb377jw4jyy">fatcat:nejow4bs3zboraiyb377jw4jyy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20160703014316/http://www.jsbi.org/pdfs/journal1/GIW09/GIW09010.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/9e/58/9e58d36d3b7c615ac843da4772501796c4013a9a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a>

Near-Native Protein Loop Sampling Using Nonparametric Density Estimation Accommodating Sparcity

Hyun Joo, Archana G. Chavan, Ryan Day, Kristin P. Lennox, Paul Sukhanov, David B. Dahl, Marina Vannucci, Jerry Tsai, Michael Levitt
<span title="2011-10-20">2011</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
Unlike the core structural elements of a protein like regular secondary structure, template based modeling (TBM) has difficulty with loop regions due to their variability in sequence and structure as well  ...  In cases with poor or few good templates (mean RMSD .7.0 Å), this sampling method produces a population of loop structures to around 3.66 Å for loops up to 17 residues.  ...  Acknowledgments We would like to thank Tien Ho for his initial input and work on this project. Author Contributions  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1002234">doi:10.1371/journal.pcbi.1002234</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22028638">pmid:22028638</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3197639/">pmcid:PMC3197639</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/t3djty5lrff77lb4m6pjhae6dq">fatcat:t3djty5lrff77lb4m6pjhae6dq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171015134343/http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002234&amp;type=printable" 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/3e/de/3ede073791654043e480b92a893fcfbbc68ff7fd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1002234"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3197639" 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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