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An Algorithm to Identify Target-Selective Ligands – A Case Study of 5-HT7/5-HT1A Receptor Selectivity
2016
PLoS ONE
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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]
2021
bioRxiv
pre-print
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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
2013
PLoS ONE
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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
2013
Bioorganic & Medicinal Chemistry
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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
2008
Journal of Computer-Aided Molecular Design
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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
2006
Drug Discovery Today : Technologies
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Combines a large number of bioactivity and screening databases http://pubchem.ncbi.nlm.nih.gov/ 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
2018
Journal of Biomedical Science
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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
2015
PLoS ONE
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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)
2019
Scientific Reports
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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
2008
International Journal of Cancer
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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
2018
Biomimetics
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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
2004
Organic and biomolecular chemistry
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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
1992
Proceedings of the National Academy of Sciences of the United States of America
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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
2007
Biochimica et Biophysica Acta - Biomembranes
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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)
2016
Journal of Cheminformatics
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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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