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Variation of geometrical and physicochemical properties in protein binding pockets and their ligands

Abdullah Kahraman, Richard J Morris, Roman A Laskowski, Janet M Thornton
<span title="">2007</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Acknowledgements The molecules in the figure were rendered using PyMOL (W.L. DeLano, http://pymol.sourceforge.net/).  ...  Each row displays different geometrical and physicochemical properties of the binding site and ligand respectively.  ...  For our current analysis we used the shape of binding pockets to test their geometrical similarity and mapped electrostatic, van der Waals and hydrophobicity potentials of the protein on the ligand surface  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-8-s8-s1">doi:10.1186/1471-2105-8-s8-s1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/n5cdpctmlvezxbzqzubr4ukyoa">fatcat:n5cdpctmlvezxbzqzubr4ukyoa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170822112228/https://link.springer.com/content/pdf/10.1186%2F1471-2105-8-S8-S1.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/33/17/33177ef86e497bc97b698fcb2b8b33a34e2b4f11.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-8-s8-s1"> <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>

Exploration of the effect of sequence variations located inside the binding pocket of HIV-1 and HIV-2 proteases

Dhoha Triki, Telli Billot, Benoit Visseaux, Diane Descamps, Delphine Flatters, Anne-Claude Camproux, Leslie Regad
<span title="2018-04-10">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
The structural comparison of PR1 and PR2 pockets highlighted structural changes induced by their sequence variations and that were consistent with these property changes.  ...  In this study, we compared the PR1 and PR2 binding pockets extracted from structures complexed with 12 ligands.  ...  ., and L.R. analysed and interpreted the data. L.R. wrote the manuscript. All authors reviewed the manuscript. All authors approved the version of the manuscript to be published.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-018-24124-5">doi:10.1038/s41598-018-24124-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29636521">pmid:29636521</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5893546/">pmcid:PMC5893546</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ztqzqc4625clbj5yw3xsq6bgte">fatcat:ztqzqc4625clbj5yw3xsq6bgte</a> </span>
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Mapping of ligand-binding cavities in proteins

C. David Andersson, Brian Y. Chen, Anna Linusson
<span title="">2009</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;
Here, we present a novel approach to characterise and map the ligand-binding cavities of proteins without direct geometric comparison of structures, based on Principal Component Analysis of cavity properties  ...  between ligand properties and ligand-binding cavity properties, tables of ligand descriptors and ligand PCA score values, statistical values and a SCREE-plot for the total ligand-binding cavity PCA, score  ...  We are grateful to Gianlucas Rossi for preparing the protein files for the SCREEN calculations.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.22655">doi:10.1002/prot.22655</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20034113">pmid:20034113</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2957484/">pmcid:PMC2957484</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/q7rjm37nefhlji3i7ljsisysdq">fatcat:q7rjm37nefhlji3i7ljsisysdq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200207044737/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC2957484&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/b7/3d/b73d244546a220420a0171fe482ca3c744aeb297.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.22655"> <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/PMC2957484" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Computational approaches to identifying and characterizing protein binding sites for ligand design

Stefan Henrich, Outi M. H. Salo-Ahen, Bingding Huang, Friedrich F. Rippmann, Gabriele Cruciani, Rebecca C. Wade
<span title="">2009</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lml5dbm4jnfmjitqk6yu3nrfd4" style="color: black;">Journal of Molecular Recognition</a> </i> &nbsp;
Geometric methods to identify pockets on protein surfaces have been developed over many years but, with new algorithms, their performance is still improving.  ...  Energetic methods can aid identification and characterization of binding pockets, and have undergone recent improvements in the treatment of solvation and hydrophobicity.  ...  Acknowledgements We gratefully acknowledge the support of the Klaus Tschira Foundation, European Union (FP 6 STREP project LIGHTS), and Biotechnology Cluster Rhein Neckar (Project INE-TP03).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/jmr.984">doi:10.1002/jmr.984</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19746440">pmid:19746440</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2wlwedwd6ndvnp76h3sc7qiagu">fatcat:2wlwedwd6ndvnp76h3sc7qiagu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20121021123139/http://www.biotec.tu-dresden.de:80/~bhuang/pdf/JMR.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/f4/c6/f4c64f72bef2704dabc385b369408c2bbacbd195.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/jmr.984"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

PyVOL: a PyMOL plugin for visualization, comparison, and volume calculation of drug-binding sites [article]

Ryan H.B. Smith, Arvin C Dar, Avner Schlessinger
<span title="2019-10-24">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Motivation: Binding pocket volumes are a simple yet important predictor of small molecule binding; however, generating visualizations of pocket topology and performing meaningful volume comparisons can  ...  Results: We developed PyVOL, a python package with a PyMOL interface and GUI, to visualize, to characterize, and to compare binding pockets.  ...  While gestalt pocket properties are useful in explaining binding site interactions, druggable pockets often are composed of distinct subpockets with very different physicochemical properties.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/816702">doi:10.1101/816702</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/t56265gsszcihiags3xiety6ye">fatcat:t56265gsszcihiags3xiety6ye</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200212211227/https://www.biorxiv.org/content/biorxiv/early/2019/10/24/816702.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/10.1101/816702"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Bioinformatics and variability in drug response: a protein structural perspective

J. L. Lahti, G. W. Tang, E. Capriotti, T. Liu, R. B. Altman
<span title="2012-05-02">2012</span> <i title="The Royal Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kdv34qlmv5gsfphm6vnme655ia" style="color: black;">Journal of the Royal Society Interface</a> </i> &nbsp;
In this review, we first summarize structural characteristics of protein targets and common mechanisms of drug interactions.  ...  Finally, we highlight tools for analysing protein structures and protein -drug interactions and discuss their application for understanding altered drug responses associated with protein structural variants  ...  There are varied structural mechanisms through which missense mutations exert their effects, such as altering the physicochemical or geometric properties of a protein binding pocket, modifying structure  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rsif.2011.0843">doi:10.1098/rsif.2011.0843</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22552919">pmid:22552919</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3367825/">pmcid:PMC3367825</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/olvu5dx4rnaahpeadr6yhntwau">fatcat:olvu5dx4rnaahpeadr6yhntwau</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190224043046/http://pdfs.semanticscholar.org/5094/77fd5b818e8fdd35db35c2271a419a58c9f8.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/50/94/509477fd5b818e8fdd35db35c2271a419a58c9f8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rsif.2011.0843"> <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/PMC3367825" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Identification of Protein–Ligand Binding Sites by the Level-Set Variational Implicit-Solvent Approach

Zuojun Guo, Bo Li, Li-Tien Cheng, Shenggao Zhou, J. Andrew McCammon, Jianwei Che
<span title="2015-01-22">2015</span> <i title="American Chemical Society (ACS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/z2ruvhjfujanbnydakuxtjslca" style="color: black;">Journal of Chemical Theory and Computation</a> </i> &nbsp;
Quantitative characterization of binding pockets with topological and physicochemical parameters was used to assess the "ligandability" of the pockets.  ...  We applied our method to a data set of 515 proteinligand complexes and found that 96.9% of the cocrystallized ligands bind to the VISM-CFA-identified pockets and that 71.8% of the identified pockets are  ...  Joachim Dzubiella for critical reading of the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/ct500867u">doi:10.1021/ct500867u</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25941465">pmid:25941465</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4410907/">pmcid:PMC4410907</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/n3e2pkkxfza77lyihocqadfvdy">fatcat:n3e2pkkxfza77lyihocqadfvdy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209152449/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4410907&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/7a/65/7a6598231075c15e15b91c68bfba985b93d66d29.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/ct500867u"> <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/PMC4410907" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Molecular Docking: From Lock and Key to Combination Lock

Tripathi A, Bankaitis VA
<span title="">2018</span> <i title="Sci Forschen, Inc."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/vnt7awxco5gijonoahwdqgked4" style="color: black;">Journal of Molecular Medicine and Clinical Applications</a> </i> &nbsp;
Acknowledgements This work was supported by grants GM44530, GM112591 from the National Institutes of Health and BE-0017 from the Robert A. Welch Foundation (VAB).  ...  We also extend our thanks to The Laboratory for Molecular Simulation and High Performance Research Computing (HPRC) at Texas A&M University for providing software, support, and computer time.  ...  dynamic physicochemical properties of the protein-ligand system.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.16966/2575-0305.106">doi:10.16966/2575-0305.106</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29333532">pmid:29333532</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5764188/">pmcid:PMC5764188</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pdkxr25v5rfmdlcl3m2x7ghzea">fatcat:pdkxr25v5rfmdlcl3m2x7ghzea</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190223111233/http://pdfs.semanticscholar.org/440d/47cf86b98dc01689c8fb3b49815334782c3e.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/44/0d/440d47cf86b98dc01689c8fb3b49815334782c3e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.16966/2575-0305.106"> <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/PMC5764188" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

From the Similarity Analysis of Protein Cavities to the Functional Classification of Protein Families Using Cavbase

Daniel Kuhn, Nils Weskamp, Stefan Schmitt, Eyke Hüllermeier, Gerhard Klebe
<span title="2006-04-25">2006</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;
We recently introduced Cavbase, a method for describing and comparing protein binding pockets on the basis of the geometrical and physicochemical properties of their active sites.  ...  In this contribution, the classification of protein binding sites using the physicochemical properties exposed to their pockets is presented.  ...  We recently introduced Cavbase, a method for describing and comparing protein binding pockets on the basis of the geometrical and physicochemical properties of their active sites.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jmb.2006.04.024">doi:10.1016/j.jmb.2006.04.024</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16697007">pmid:16697007</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7094329/">pmcid:PMC7094329</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/apfzxd7gtbbchalkaqlf3kqpu4">fatcat:apfzxd7gtbbchalkaqlf3kqpu4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200328231259/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC7094329&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/79/24/79246e2ed646afb4c999dd767475991807ac4a32.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jmb.2006.04.024"> <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/PMC7094329" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison

Lee Sael, Daisuke Kihara
<span title="2012-01-24">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 pocket surface is extracted by casting rays from the center of the ligand binding pocket after the protein surface properties are computed.  ...  Function of a protein, specifically, small ligand molecules that bind to a protein, can be predicted by finding similar local surface regions in binding sites of known proteins.  ...  This work is supported by the National Institute of General Medical Sciences of the National Institutes of Health (R01GM075004).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.24018">doi:10.1002/prot.24018</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22275074">pmid:22275074</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3294165/">pmcid:PMC3294165</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/x4dny7aqsbevjo62muy77cjxxu">fatcat:x4dny7aqsbevjo62muy77cjxxu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20120712182816/http://dragon.bio.purdue.edu/paper/PatchSurfer_Proteins.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/58/76/587611a64ffb66b2cd9caa08698bf4bd033e0528.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.24018"> <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/PMC3294165" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Scaling the Druggability Landscape of Human Bromodomains, a New Class of Drug Targets

Guangtao Zhang, Roberto Sanchez, Ming-Ming Zhou
<span title="2012-08-28">2012</span> <i title="American Chemical Society (ACS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/biqbvvfsgzd3tgqsg6hhdhdk2u" style="color: black;">Journal of Medicinal Chemistry</a> </i> &nbsp;
the acetyl-lysine binding pocket. 2 Given high degree variations in the amino acid sequence and structural flexibility of the ZA and BC loops, the acetyl-lysine binding pocket poses a challenge to developing  ...  In an effort to explore the physicochemical basis for small molecule inhibition of bromodomains, Vidler et al conducted a family-wide survey of the druggability landscape of the acetyl-lysine binding site  ...  Acknowledgments The work was in part supported by the grants from the National Institutes of Health (to M.-M.Z.).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/jm3011977">doi:10.1021/jm3011977</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22928775">pmid:22928775</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3454531/">pmcid:PMC3454531</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ru2f3l4povfshai3msdt3pe3wa">fatcat:ru2f3l4povfshai3msdt3pe3wa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200210044938/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3454531&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/d4/37/d43773c13494b24eba4db0e0819745645f04845b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/jm3011977"> <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/PMC3454531" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Conformational readout of RNA by small ligands

Efrat Kligun, Yael Mandel-Gutfreund
<span title="">2013</span> <i title="Informa UK Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2gz5p7hhszcttc2a7kuvirxupu" style="color: black;">RNA Biology</a> </i> &nbsp;
We analyzed the chemical, physical, structural and conformational properties of binding pockets around the ligand. comparing the properties of ligand-binding pockets to the properties of computed pockets  ...  The increasing number of available RNA structures, in complex with proteins, small ligands and in free form, enables the design of new therapeutically useful RNA-binding ligands. here we studied RNA ligand  ...  of the different physicochemical properties in the binding pockets relative to background.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4161/rna.24682">doi:10.4161/rna.24682</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23618839">pmid:23618839</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4111737/">pmcid:PMC4111737</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/77n4tj2jizbsvkuzcj2jnr3db4">fatcat:77n4tj2jizbsvkuzcj2jnr3db4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20130925224522/http://yaelab.technion.ac.il/papers/Kligun_2013.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/ff/98/ff98bbd5d3abf149e3002c67af2eb4984a26031d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4161/rna.24682"> <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/PMC4111737" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Bridging protein local structures and protein functions

Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, Luonan Chen
<span title="2008-04-18">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/spfkqu35dnd7rjl5ooxt2ihb4q" style="color: black;">Amino Acids</a> </i> &nbsp;
In this review, we summarize the repertoire of methods currently being applied and report recent progress in the field of in silico annotation of protein function based on the accumulation of vast amounts  ...  In particular, we emphasize the newly developed structure-based methods, which are able to identify locally structural motifs and reveal their relationship with protein functions.  ...  Acknowledgments This work was supported by the National Natural Science Foundation of China (NSFC) under Grant No. 10631070 and No. 60503004.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00726-008-0088-8">doi:10.1007/s00726-008-0088-8</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18421562">pmid:18421562</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/micrifjcrfetnafnm4fx45ouom">fatcat:micrifjcrfetnafnm4fx45ouom</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200321152145/http://zhangroup.aporc.org/images/files/aminoacidweb.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/c9/53/c9532d4fdff5aea4044eba3830c6854ee1c4acfa.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00726-008-0088-8"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets

Antonia Stank, Daria B. Kokh, Max Horn, Elena Sizikova, Rebecca Neil, Joanna Panecka, Stefan Richter, Rebecca C. Wade
<span title="2017-04-20">2017</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;
The TRAnsient Pockets in Proteins (TRAPP) webserver provides an automated workflow that allows users to explore the dynamics of a protein binding site and to detect pockets or sub-pockets that may transiently  ...  --detection, analysis, and visualization of the binding pocket dynamics and characteristics, such as volume, solvent-exposed area or properties of surrounding residues.  ...  ACKNOWLEDGEMENTS We thank the members of the Molecular and Cellular Modeling group at HITS for testing the TRAPP webserver, and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkx277">doi:10.1093/nar/gkx277</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28431137">pmid:28431137</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5570179/">pmcid:PMC5570179</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/got7nfeosrfevpgnrjcwx4zl5i">fatcat:got7nfeosrfevpgnrjcwx4zl5i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190220091916/http://pdfs.semanticscholar.org/21c0/ba177ec29a40f89ac03c1976bfce0f7d553b.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/c0/21c0ba177ec29a40f89ac03c1976bfce0f7d553b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkx277"> <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/PMC5570179" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Classification of protein functional surfaces using structural characteristics

Y. Y. Tseng, W.-H. Li
<span title="2012-01-11">2012</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;
As an expandable library, PSC provides a resource of spatial patterns for studying the evolution of protein structure and function. geometric matching | split pocket | structural footprinting | physicochemical  ...  In conclusion, our approach complements the sequence-based and fold-domain classifications and has the advantage of associating the shape of a protein with its biological function.  ...  We thank Ariel Fernandez, Robert Friedman, and Ilya Vakser for valuable comments and suggestions. This study was supported by National Institutes of Health Grant GM30998.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.1119684109">doi:10.1073/pnas.1119684109</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22238424">pmid:22238424</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3268291/">pmcid:PMC3268291</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ximmszu3rjazfgspplsirfbuxq">fatcat:ximmszu3rjazfgspplsirfbuxq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190224075546/http://pdfs.semanticscholar.org/5ed1/8b59014535904fd15fc23f775300db6165ae.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/5e/d1/5ed18b59014535904fd15fc23f775300db6165ae.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.1119684109"> <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/PMC3268291" 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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