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Using more than 801 296 small-molecule crystal structures to aid in protein structure refinement and analysis

Jason C. Cole, Ilenia Giangreco, Colin R. Groom
<span title="2017-02-22">2017</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;
The Cambridge Structural Database (CSD) is the worldwide resource for the dissemination of all published three-dimensional structures of small-molecule organic and metal–organic compounds.  ...  Examples highlight how the CSD and associated software aid protein–ligand complex validation, and show how the CSD could be further used in the generation of geometrical restraints for protein structure  ...  This work would not be possible without the exemplary sharing of structures by the small-molecule crystallographic community.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s2059798316014352">doi:10.1107/s2059798316014352</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28291758">pmid:28291758</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5349435/">pmcid:PMC5349435</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ndf5no5omfhhrpb5gpzqlwy2wm">fatcat:ndf5no5omfhhrpb5gpzqlwy2wm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724035400/http://journals.iucr.org/d/issues/2017/03/00/ba5250/ba5250.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/10/03/1003de964504724574fc3032d219647c8512ae7b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s2059798316014352"> <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/PMC5349435" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Life-science applications of the Cambridge Structural Database

Robin Taylor
<span title="2002-05-29">2002</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;
Torsional distributions derived from the Cambridge Structural Database (CSD) can be used to map out potential-energy surfaces and thereby help identify experimentally validated conformational minima of  ...  The use of crystallographic data in this way is complementary toin vacuotheoretical calculations since it gives insights into conformational preferences in condensed-phase situations.  ...  All staff of the Cambridge Crystallographic Data Centre, past and present, are thanked for their efforts in building and maintaining the CSD System.  ... 
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<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809135232/http://www.dddc.ac.cn/embo04/material/Taylor_2002.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/85/2a/852add4bba8b8e86b8bfdd2f538719a44480d0a3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s090744490200358x"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Conformational Variability of Benzamidinium-Based Inhibitors

Xue Li, Xiao He, Bing Wang, Kenneth Merz
<span title="2009-06-10">2009</span> <i title="American Chemical Society (ACS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/czzozsmlgreapacsfn45462e54" style="color: black;">Journal of the American Chemical Society</a> </i> &nbsp;
The preferred conformation of a small molecule can change when bound to a protein, and a detailed knowledge of the preferred conformation(s) of a bound ligand can help in optimizing the affinity of a molecule  ...  quite suitable for modeling proteins often are less suitable for small molecule structures due to a lack of validated parameters.  ...  We thank the NIH for supporting this research via NIH grants GM044974 and GM066859.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/ja9010833">doi:10.1021/ja9010833</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19435349">pmid:19435349</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2730048/">pmcid:PMC2730048</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eji2mxxqkjftrf3yalewqrtfji">fatcat:eji2mxxqkjftrf3yalewqrtfji</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200501165959/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC2730048&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/76/f7/76f7ac8f5a8fb93360619b68ea179b83357a0fee.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/ja9010833"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acs.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2730048" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe Ç

Thomas E. Edwards, Pavol Cekan, Gunnar W. Reginsson, Sandip A. Shelke, Adrian R. Ferré-D'Amaré, Olav Schiemann, Snorri Th. Sigurdsson
<span title="2011-01-19">2011</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;
To understand the effect of Ç on nucleic acid structure, we undertook a detailed crystallographic analysis.  ...  These results indicate a small degree of flexibility around the oxazine linkage, which may be a consequence of the antiaromaticity of a 16-n electron ring system.  ...  on c¸in the planar conformation as found in the small molecule crystal structure of 1.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr015">doi:10.1093/nar/gkr015</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21252294">pmid:21252294</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3105401/">pmcid:PMC3105401</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xfi7pvw73zbzbelk7xntdsbnxi">fatcat:xfi7pvw73zbzbelk7xntdsbnxi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190308113455/http://pdfs.semanticscholar.org/f23e/45e7b177c12593164430ffbb164544c41f18.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/f2/3e/f23e45e7b177c12593164430ffbb164544c41f18.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr015"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105401" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Nucleic acid solvation: from outside to insight

Pascal Auffinger, Yaser Hashem
<span title="">2007</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/uzv6ve6frfevrcjkqzfvw36bfu" style="color: black;">Current Opinion in Structural Biology</a> </i> &nbsp;
Nucleic acids are polyanionic molecules that were historically considered to be solely surrounded by a shell of water molecules and a neutralizing cloud of monovalent and divalent cations.  ...  In this respect, recent experimental and theoretical reports demonstrate that water molecules within complex nucleic acid structures can display very long residency times, and assist drug binding and catalytic  ...  Acknowledgements The authors wish to thank Neena Grover for reading the manuscript and for interesting discussions, and Eric Westhof for ongoing support.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.sbi.2007.05.008">doi:10.1016/j.sbi.2007.05.008</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17574833">pmid:17574833</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6cchirelkjandauw4cn5qutx2u">fatcat:6cchirelkjandauw4cn5qutx2u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200709234015/http://www-ibmc.u-strasbg.fr/arn/Westhof/publ_West/bib2007/r2007_PAuffinger_COSB.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/f0/8a/f08abc793a25c8f6b12903f8b3b74de3ce5fe071.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.sbi.2007.05.008"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

You are lost without a map: Navigating the sea of protein structures

Audrey L. Lamb, T. Joseph Kappock, Nicholas R. Silvaggi
<span title="">2015</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zsupycdufvggvpoal5g3x5zi2a" style="color: black;">Biochimica et Biophysica Acta - Proteins and Proteomics</a> </i> &nbsp;
Crystallographers mainly rely on "global" measures of data and model quality to build models.  ...  Robust validation procedures based on global measures now largely ensure that structures in the Protein Data Bank (PDB) are largely correct.  ...  The first step is to understand how crystallographic models are made.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bbapap.2014.12.021">doi:10.1016/j.bbapap.2014.12.021</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25554228">pmid:25554228</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5051661/">pmcid:PMC5051661</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/w6qjtbkdbbdd5iu3cttyol2aay">fatcat:w6qjtbkdbbdd5iu3cttyol2aay</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719151041/https://kuscholarworks.ku.edu/bitstream/handle/1808/22037/Lamb_2016_HHSPubAccess.pdf;jsessionid=FAA85A59D207B4020F0C2EFA1921C393?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d0/6e/d06ec1158c3a863409e581ccd05c75a25d6ca30c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bbapap.2014.12.021"> <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/PMC5051661" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Carbohydrate anomalies in the PDB

Jon Agirre, Gideon Davies, Keith Wilson, Kevin Cowtan
<span title="">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/addogasjsnb6veviekj3hbmsw4" style="color: black;">Nature Chemical Biology</a> </i> &nbsp;
(cross validation, deposition of coordinates and data, etc.).  ...  When such small molecules are present in macromolecule structures, they are often reported with stereo and region-chemical errors and in unlikely conformations.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nchembio.1798">doi:10.1038/nchembio.1798</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25885951">pmid:25885951</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/l5jfzbp2t5hxnfmnug62xqnhxi">fatcat:l5jfzbp2t5hxnfmnug62xqnhxi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190218124734/http://pdfs.semanticscholar.org/0bc4/cc21abbd037937a30b7122ab3932f92fe939.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/0b/c4/0bc4cc21abbd037937a30b7122ab3932f92fe939.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nchembio.1798"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> nature.com </button> </a>

Database research in crystal engineering

Ashwini Nangia
<span title="">2002</span> <i title="Royal Society of Chemistry (RSC)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rv24nnf5ibdcnj66kxmakzl3cu" style="color: black;">CrysteEngComm</a> </i> &nbsp;
The approach geometry of hydrogen bond donors to various functional groups derived from small-molecule crystal structures is used as a model in structure-based drug design and pharmacophore mapping.  ...  Statistical analysis of structural data provides a better understanding of the nature of hydrogen bonds and intermolecular interactions and facilitates in the identification of frequently occurring interaction  ...  Acknowledgements The author thanks the Department of Science and Technology, Government of India, for research funding (Project No. SP/S1/ G-29/98).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/b201206e">doi:10.1039/b201206e</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jd7vkfx7bfeivpiilk7iyrngbi">fatcat:jd7vkfx7bfeivpiilk7iyrngbi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20060207011459/http://202.41.85.161:80/~an/Articles/an02_cec_1.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/b9/b5/b9b5050c0c6a6b4927170ee8fceb03c85b4a3edc.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/b201206e"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Small Molecule Crystallography in Drug Design

Johan Wouters, Frederic Ooms
<span title="2001-05-01">2001</span> <i title="Bentham Science Publishers Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xtiwjcbzsbd35jtqmz56mrpmb4" style="color: black;">Current pharmaceutical design</a> </i> &nbsp;
Indeed, structural data obtained from small molecules crystallography can approach ligand-receptor binding by providing unique structural features both about the conformation (internal geometry) of the  ...  Small molecule crystal structure databases can also be used in three dimensional search to identify new drug candidates.  ...  Indeed, small molecule crystal structures and crystallographic structure databases can provide information on both the bio-active conformation of ligands and on functional groups essential for the interaction  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/1381612013397889">doi:10.2174/1381612013397889</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11375767">pmid:11375767</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eph3d7yysvfvhln4eepcwwus4y">fatcat:eph3d7yysvfvhln4eepcwwus4y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20040321125153/http://www.fundp.ac.be:80/~jwouters/CV/JohanWouters.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/a0/afa050636d4500427531e635b184b8eff4243bd0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/1381612013397889"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Crystallographic curiosities: polymorphism and structures with Z′ > 1

William Clegg
<span title="2019-06-24">2019</span> <i title="International Union of Crystallography (IUCr)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6wwt7s6j4fgvjm446w6563lwwa" style="color: black;">Acta Crystallographica Section C Structural Chemistry</a> </i> &nbsp;
It has been extensively used for studies of molecular conformation, analyses of intermolecular interactions, modelling of some kinds of chemical reaction pathways, and the generation of average and idealized  ...  Among these are the topics of polymorphism -the occurrence of more than one crystal structure for a given chemical compound -and the incidence of structures with more than one molecule, unrelated by crystallographic  ...  AE25 of 180 are over 85% of the total, and almost all others have two thiophene rings, validating this model.)  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s2053229619008799">doi:10.1107/s2053229619008799</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5epyfbb46vfldmndpepffc73di">fatcat:5epyfbb46vfldmndpepffc73di</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200307131735/https://journals.iucr.org/c/issues/2019/07/00/me6041/me6041.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/2e/a3/2ea358c71c960943ad78a1319068207e52176422.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s2053229619008799"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Structure and location of amiodarone in a membrane bilayer as determined by molecular mechanics and quantitative x-ray diffraction

M. Trumbore, D.W. Chester, J. Moring, D. Rhodes, L.G. Herbette
<span title="">1988</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
Small angle x-ray diffraction was used to determine the position of the iodine atoms of amiodarone in dipalmitoylphosphatidylcholine (DPPC) lipid bilayers under conditions of low temperature and hydration  ...  This type of analysis promises to be of great use in the design of drugs with greater potency and higher specificity.  ...  Katz for discussions regarding drugmembrane interactions which allowed us to relate these results to clinical questions. We also thank Dr. P.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0006-3495(88)82986-2">doi:10.1016/s0006-3495(88)82986-2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/3207838">pmid:3207838</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1330352/">pmcid:PMC1330352</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gpz6452dpfbi3lk3oglvxh76jy">fatcat:gpz6452dpfbi3lk3oglvxh76jy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170927192840/http://publisher-connector.core.ac.uk/resourcesync/data/elsevier/pdf/58e/aHR0cDovL2FwaS5lbHNldmllci5jb20vY29udGVudC9hcnRpY2xlL3BpaS9zMDAwNjM0OTU4ODgyOTg2Mg%3D%3D.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/36/a9/36a96fb3be36900ebd42979983a4fb5007225d31.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0006-3495(88)82986-2"> <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/PMC1330352" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

In-crystal affinity ranking of fragment hit compounds reveals a relationship with their inhibitory activities

Junji Yamane, Min Yao, Yong Zhou, Yasuyuki Hiramatsu, Kenichiro Fujiwara, Tohru Yamaguchi, Hiroto Yamaguchi, Hiroko Togame, Hideki Tsujishita, Hiroshi Takemoto, Isao Tanaka
<span title="2011-06-08">2011</span> <i title="International Union of Crystallography (IUCr)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cwa7fmuhpjemdknjvjrxvpyaze" style="color: black;">Journal of Applied Crystallography</a> </i> &nbsp;
The crystallographic validation methodology described here will greatly accelerate the hit-to-lead process during fragment-based and structure-based drug design.  ...  To address this issue, crystallographic competition experiments were carried out to determine the relative order of the in-crystal binding affinities using five hit compounds of bovine pancreatic trypsin  ...  Hattori and Y. Sakou (Shionogi & Co. Ltd) for valuable scientific discussions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s0021889811017717">doi:10.1107/s0021889811017717</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/p3e3rudvnzduraghl6sbpblwz4">fatcat:p3e3rudvnzduraghl6sbpblwz4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170815180103/https://eprints.lib.hokudai.ac.jp/dspace/bitstream/2115/46908/1/JAC44-4_798-804.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/e0/a4/e0a4a7cd04040f0062d696fc975b3028116a3781.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s0021889811017717"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Comparing protein-ligand interactions in solution and single crystals by Raman spectroscopy

M. D. Altose, Y. Zheng, J. Dong, B. A. Palfey, P. R. Carey
<span title="2001-03-06">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;
In general, the ability to compare detailed Raman data for complexes in crystals and solution provides a means of bridging crystallographic and solution studies.  ...  ring are not identical in the two phases.  ...  Although it is valid to discuss intensity changes in isoalloxazine ring modes for the in and out conformers in solution, it is difficult to make the same comparison for the crystal forms.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.061029598">doi:10.1073/pnas.061029598</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11248022">pmid:11248022</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC30597/">pmcid:PMC30597</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7jxaprngerhp5dify2rpgb2pom">fatcat:7jxaprngerhp5dify2rpgb2pom</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191123002618/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC30597&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/94/68/9468117036c4dad6da8fbf80bf516197efcbc7f1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.061029598"> <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/PMC30597" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The role of lone pair and dipolar interactions in the non-planarity of 1,3-dioxolane and 1,3-dioxole

Vernon G. S. Box
<span title="">2001</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;
A new study of 1,3-dioxole, 1,3-dioxolane, tetrahydrofuran, cyclopentane, and some related molecules using the new QVBMM (molecular mechanics) force field shows conclusively that the non-planarity of 1,3  ...  Subsequently, an ab initio theoretical study of this molecule was performed, which also concluded that the non-planarity of 1,3-dioxole was due to the anomeric effect and not to dipole-dipole interactions  ...  Note the close correspondence between the QVBMM predicted data and the X-ray crystallographic data for tetrahydrofuran (2) and, in particular, note the correspondence between the bond lengths for the  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s008940100030">doi:10.1007/s008940100030</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3xp3feqldjbnrjdkpcx6iazxsm">fatcat:3xp3feqldjbnrjdkpcx6iazxsm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20040706162122/http://www.chemia.uj.edu.pl:80/~migda/Literatura/pdf/10070193.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/2a/cf/2acfb0086a3a44d668d4cb4afdadc2f8bb97f9c4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s008940100030"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

The PDZ2 Domain of Syntenin at Ultra-high Resolution: Bridging the Gap Between Macromolecular and Small Molecule Crystallography

Beom Sik Kang, Yancho Devedjiev, Urszula Derewenda, Zygmunt S. Derewenda
<span title="">2004</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nk6zopmzsjfizb6z5kztdu477y" style="color: black;">Journal of Molecular Biology</a> </i> &nbsp;
The crystal structure of the second PDZ domain of the scaffolding protein syntenin was solved using data extending to 0.73 Å resolution.  ...  The crystallographic model, including the hydrogen atoms and the anisotropic displacement parameters, was refined to a conventional R-factor of 7.5% and R free of 8.7%, making it the most precise crystallographic  ...  Acknowledgements Data collection for this study at the NSLS (Brookhaven National Laboratory, Upton, New York) was carried out during RapiData2003, a practical course in macromolecular X-ray diffraction  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jmb.2004.02.057">doi:10.1016/j.jmb.2004.02.057</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15081807">pmid:15081807</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/whekofqevjfctgnpf3ts6nmvdq">fatcat:whekofqevjfctgnpf3ts6nmvdq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20050223104640/http://www.ices.utexas.edu:80/%7Ejunli/motif/ps/PDZ2.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/20/5c/205ca15a2441d7c68287296c133f4de2e2ec5df2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jmb.2004.02.057"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>
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