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An Algorithm to Identify Target-Selective Ligands – A Case Study of 5-HT7/5-HT1A Receptor Selectivity

Rafał Kurczab, Vittorio Canale, Paweł Zajdel, Andrzej J. Bojarski, Alexey Porollo
2016 PLoS ONE  
A computational procedure to search for selective ligands for structurally related protein targets was developed and verified for serotonergic 5-HT 7 /5-HT 1A receptor ligands.  ...  The combination of two approaches of data representation (molecular fingerprints vs. structural interaction fingerprints), different training set sizes and selection of the best SVM component models for  ...  Next, the interaction fingerprints (SIFt) were calculated for all obtained ligand-receptor complexes.  ... 
doi:10.1371/journal.pone.0156986 pmid:27271158 pmcid:PMC4896471 fatcat:jdbhffsjhjcdzcudqczdymz42e

fingeRNAt - a novel tool for high-throughput analysis of nucleic acid-ligand interactions [article]

Natalia Anna Szulc, Zuzanna Mackiewicz, Janusz M Bujnicki, Filip Stefaniak
2021 bioRxiv   pre-print
Interactions are also encoded and stored as a bioinformatics-friendly Structural Interaction Fingerprint (SIFt) - a binary string where the respective bit in the fingerprint is set to 1 if a particular  ...  Here, we introduce fingeRNAt - a software tool for detecting non-covalent interactions formed in complexes of nucleic acids with ligands.  ...  This research was carried out in part with the support of the Interdisciplinary Centre for Mathematical and Computational Modelling (ICM) University of Warsaw under computational allocation no GB76-20  ... 
doi:10.1101/2021.12.23.474073 fatcat:youpubtszfaidcu22wiyh4ppre

Human Thromboxane A2 Receptor Genetic Variants: In Silico, In Vitro and "In Platelet" Analysis

Scott Gleim, Jeremiah Stitham, Wai Ho Tang, Hong Li, Karen Douville, Prashen Chelikani, Jeffrey J.Rade, Kathleen A. Martin, John Hwa, James Porter
2013 PLoS ONE  
In the absence of patient platelet samples, we developed and validated a novel megakaryocyte based system to evaluate human platelet function in the presence of detected dysfunctional genetic variants.  ...  involved in receptor function and in silico predictions.  ...  Based on a PSI-BLAST search alignment, SIFT returns a scaled probability matrix for the likelihood of a protein to tolerate each of the twenty amino acids at each position in the protein.  ... 
doi:10.1371/journal.pone.0067314 pmid:23840660 pmcid:PMC3696120 fatcat:p7bnmrxoebesthkol4r3l4nh4y

A sphingosine 1-phosphate receptor 2 selective allosteric agonist

Hideo Satsu, Marie-Therese Schaeffer, Miguel Guerrero, Adrian Saldana, Christina Eberhart, Peter Hodder, Charmagne Cayanan, Stephan Schürer, Barun Bhhatarai, Ed Roberts, Hugh Rosen, Steven J. Brown
2013 Bioorganic & Medicinal Chemistry  
Mutation of receptor residues responsible for binding to the zwitterionic headgroup of sphingosine 1-phosphate (S1P) abolishes S1P activation of the receptor, but not activation by CYM-5520.  ...  These compounds, XAX-162 and CYM-5520, are highly selective and do not activate other S1P receptors. Binding of CYM-5520 is not competitive with the antagonist JTE-013.  ...  These data include MOL files and InChiKeys of the most important compounds described in this article.  ... 
doi:10.1016/j.bmc.2013.06.012 pmid:23849205 pmcid:PMC3786410 fatcat:omfs2ueturbahiwedywh2monly

Interaction force diagrams: new insight into ligand-receptor binding

Hooman Shadnia, James S. Wright, James M. Anderson
2008 Journal of Computer-Aided Molecular Design  
A method is described to calculate and visualize the interaction forces of ligand-receptor complexes.  ...  The latter representation leads to definition of an "Interaction Force Fingerprint" (IFFP) which is characteristic of the ligand-receptor binding.  ...  The most significant interactions produced in this way are schematically represented on 2D diagrams of the protein-ligand complex. COMBINE on the other hand, uses a more elaborate approach.  ... 
doi:10.1007/s10822-008-9250-3 pmid:18989626 fatcat:i56gvnksundjlmgv3wddngpelm

In silico target fishing: Predicting biological targets from chemical structure

Jeremy L. Jenkins, Andreas Bender, John W. Davies
2006 Drug Discovery Today : Technologies  
Combines a large number of bioactivity and screening databases ChemBank A public, web-based service from the Broad Institute's Chemical Biology Program.  ...  We provide a comparative review of recent studies in which data mining, similarity, or docking of chemical structures is used to elucidate target class or mechanism of action.  ...  Acknowledgements We thank Meir Glick, Jim Nettles, Zhan Deng, Nidhi, Thomas Crisman, Ansgar Schuffenhauer, John Peter Priestle, Kamal Azzaoui, Edgar Jacoby, John Tallarico, Bernd Rohde, Dmitri Mikhailov of  ... 
doi:10.1016/j.ddtec.2006.12.008 fatcat:7p6uljq43balfmxczca7eb7joi

Novel mutation G324C in WNT1 mapped in a large Pakistani family with severe recessively inherited Osteogenesis Imperfecta

Mehran Kausar, Saima Siddiqi, Muhammad Yaqoob, Sajid Mansoor, Outi Makitie, Asif Mir, Chiea Chuen Khor, Jia Nee Foo, Mariam Anees
2018 Journal of Biomedical Science  
Conclusion: We report a novel mutation responsible for OI and our investigation expands the spectrum of diseasecausing WNT1 mutations and the resulting OI phenotypes.  ...  The present study was conducted to determine the underlying genetic cause of an autosomal recessive skeletal dysplasia in a large consanguineous family from Chinute, Pakistan.  ...  We also thank Wee Yang Meah and Hui-Meng Soo from the Genome Institute of Singapore for their help with the genotyping and sequencing of the samples.  ... 
doi:10.1186/s12929-018-0481-x fatcat:pkhx4feta5brljxn243kwvpboa

Analysing the Effect of Mutation on Protein Function and Discovering Potential Inhibitors of CDK4: Molecular Modelling and Dynamics Studies

Nagasundaram N, Hailong Zhu, Jiming Liu, Karthick V, George Priya Doss C, Chiranjib Chakraborty, Luonan Chen, Freddie Salsbury
2015 PLoS ONE  
interactions.  ...  In this study, we used a systematic, integrated computational approach to identify deleterious nsSNPs and predict their effects on protein-protein (CDK4cyclin D1) and protein-ligand (CDK4-flavopiridol)  ...  Notably, no interaction was observed with the ATP binding residues of R210P (Fig 2C and 2D ).  ... 
doi:10.1371/journal.pone.0133969 pmid:26252490 pmcid:PMC4529227 fatcat:orskjkpb2nak7ch3neoxlwxiqq

Rigorous sampling of docking poses unveils binding hypothesis for the halogenated ligands of L-type Amino acid Transporter 1 (LAT1)

Natesh Singh, Bruno O. Villoutreix, Gerhard F. Ecker
2019 Scientific Reports  
First, a homology model of LAT1 based on the atomic structure of a prokaryotic homolog was constructed. Docking studies using a set of halogenated ligands allowed for deriving a binding hypothesis.  ...  Collectively, the results highlight the dual nature of the ligand-protein binding mode characterized by backbone hydrogen bond interactions of the amino acid moiety of the ligands and residues I63, S66  ...  Acknowledgements We thank the Région Hauts-de-France, University of Lille, Inserm institute for financial supports.  ... 
doi:10.1038/s41598-019-51455-8 pmid:31636293 pmcid:PMC6803698 fatcat:pcr4gvpgejhsrp75wijnuok6ni

Breast cancer-associated mutations in metalloprotease disintegrin ADAM12 interfere with the intracellular trafficking and processing of the protein

Emilia Dyczynska, Emilia Syta, Danqiong Sun, Anna Zolkiewska
2008 International Journal of Cancer  
Consequently, the D/H and G/E mutants, unlike the wild-type ADAM12, are not capable of shedding Delta-like l, a ligand for Notch receptor, at the cell surface, or of stimulating cell migration.  ...  ADAM12 has recently emerged as a Candidate Cancer Gene in a comprehensive genetic analysis of human breast cancers.  ...  Abbreviations ADAM, protein containing a disintegrin and metalloprotease; Dll1, Delta-like 1; DMEM, Dulbecco's modified Eagle's medium; DPBS, Dulbecco's phosphate-buffered saline; FBS, fetal bovine serum  ... 
doi:10.1002/ijc.23405 pmid:18241035 pmcid:PMC2636846 fatcat:jyljqci7ebenfj2prdxs5lc24y

Alterations in Cellular Processes Involving Vesicular Trafficking and Implications in Drug Delivery

Silvia Muro
2018 Biomimetics  
This article offers a critical overview of these topics, discussing current achievements, limitations and future perspectives on the use of vesicular transport for drug delivery applications.  ...  From a translational perspective, they offer avenues to improve the access of therapeutic drugs across cellular barriers that separate body compartments and into diseased cells.  ...  integral proteins such as receptors being recycled, or drugs which partition within the membrane; or (iii) be transported via interacting with a membrane component, such as a ligand or targeted drug-carrier  ... 
doi:10.3390/biomimetics3030019 pmid:31105241 pmcid:PMC6352689 fatcat:coda6uusvjgxpg7oai35oqsfxy

Molecular similarity: a key technique in molecular informatics

Andreas Bender, Robert C. Glen
2004 Organic and biomolecular chemistry  
Molecular similarity, as a paradigm, contains many implicit and explicit assumptions in particular with respect to the prediction of the binding and efficacy of molecules at biological receptors.  ...  T h i s j o u r n a l i s © T h e R o y a l S o c i e t y o f C h e m i s t r y 2 0 0 4 3 2 0 4 O r g . B i o m o l .  ...  A number of anonymous referees are thanked for providing valuable input on the manuscript.  ... 
doi:10.1039/b409813g pmid:15534697 fatcat:sci2mbt3p5frhklzytvsiavp5m

Estrogen receptors colocalize with low-affinity nerve growth factor receptors in cholinergic neurons of the basal forebrain

C. D. Toran-Allerand, R. C. Miranda, W. D. Bentham, F. Sohrabji, T. J. Brown, R. B. Hochberg, N. J. MacLusky
1992 Proceedings of the National Academy of Sciences of the United States of America  
Estrogen receptors colocalize with low-affinity nerve growth factor receptors in cholinergic neurons of the basal forebrain (steroid autoradography/nonlsotopIc iu sift hybrdatlou/mo tohe sty/c t/aglng  ...  Colocalization of estrogen and low-affinity nerve growth factor receptors implies that their ligands may act on the same neuron, perhaps synergistically, to regulate the expression of specific genes or  ...  Patricia Goldman-Rakic, Lloyd A. Greene, Carol A. Mason, and Anne-Judith Silverman for their helpful comments and E. M. Johnson, Jr., for the gift of monoclonal antibody IgG 192.  ... 
doi:10.1073/pnas.89.10.4668 pmid:1316615 pmcid:PMC49144 fatcat:7ix3p6gsbrfhtcszgkxdvdsstq

Structural analysis of pituitary adenylate cyclase-activating polypeptides bound to phospholipid membranes by magic angle spinning solid-state NMR

Nobuyasu Komi, Kayo Okawa, Yukihiro Tateishi, Masahiro Shirakawa, Toshimichi Fujiwara, Hideo Akutsu
2007 Biochimica et Biophysica Acta - Biomembranes  
PACAP (pituitary adenylate cyclase-activating polypeptide) is a member of the VIP/secretin/glucagon family, which includes the ligands of class II G-protein coupled receptors.  ...  Since the recognition of PACAP by the receptor may involve the binding of PACAP to membranes, its membrane-bound structure should be important.  ...  This work was partly supported by Grants-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Science, Technology, Sport and Culture of Japan (HA and MS), and grants from JST  ... 
doi:10.1016/j.bbamem.2007.10.015 pmid:17996724 fatcat:vbsbsjonijekdpu4itzbdo7xa4

11th German Conference on Chemoinformatics (GCC 2015)

Uli Fechner, Chris de Graaf, Andrew E. Torda, Stefan Güssregen, Andreas Evers, Hans Matter, Gerhard Hessler, Nicola J. Richmond, Peter Schmidtke, Marwin H. S. Segler, Mark P. Waller, Stefanie Pleik (+248 others)
2016 Journal of Cheminformatics  
by means of the SIFt algorithm [2] .  ...  The combination of all 3 different approaches was optimized to a workflow that produces a reliable structural model, useful for a meaningful analysis of ligand-receptor interactions, not seen in the original  ...  Human FKBPs play miscellaneous roles, as for example in the regulation of steroid hormone receptor function and the immune response.  ... 
doi:10.1186/s13321-016-0119-5 pmid:29270804 pmcid:PMC4896257 fatcat:akoqbbe6fvc5bgc6qwnxqhiaya
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