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MSV3d: database of human MisSense variants mapped to 3D protein structure

T.-D. Luu, A.-M. Rusu, V. Walter, R. Ripp, L. Moulinier, J. Muller, T. Toursel, J. D. Thompson, O. Poch, H. Nguyen
2012 Database: The Journal of Biological Databases and Curation  
We present MSV3d (Database of human MisSense Variants mapped to 3D protein structure), a new database that contains detailed annotation of missense variants of all human proteins (20 199 proteins).  ...  The elucidation of the complex relationships linking genotypic and phenotypic variations to protein structure is a major challenge in the post-genomic era.  ...  Acknowledgements The authors are grateful to Serge Uge for his assistance in implementing the local cluster. The IGBMC common services and platforms are acknowledged for assistance.  ... 
doi:10.1093/database/bas018 pmid:22491796 pmcid:PMC3317913 fatcat:yrpykuh6prev3bxaj4jq2wovzm

KD4v: comprehensible knowledge discovery system for missense variant

Tien-Dao Luu, Alin Rusu, Vincent Walter, Benjamin Linard, Laetitia Poidevin, Raymond Ripp, Luc Moulinier, Jean Muller, Wolfgang Raffelsberger, Nicolas Wicker, Odile Lecompte, Julie D. Thompson (+2 others)
2012 Nucleic Acids Research  
The server provides a set of rules learned by Induction Logic Programming (ILP) on a set of missense variants described by conservation, physico-chemical, functional and 3D structure predicates.  ...  The KD4v (Comprehensible Knowledge Discovery System for Missense Variant) server allows to characterize and predict the phenotypic effects (deleterious/neutral) of missense variants.  ...  We applied the ILP method (9) to a set of nsSNPs involved in human diseases that are mapped to 3D structure and annotated by the MSV3d (MisSense Variant mapped to 3D structure) pipeline (10) .  ... 
doi:10.1093/nar/gks474 pmid:22641855 pmcid:PMC3394327 fatcat:w3ri226mdbfsllra5tay3rsbfu

Knowledge Discovery in Variant Databases Using Inductive Logic Programming

Hoan Nguyen, Tien-Dao Luu, Olivier Poch, Julie D. Thompson
2013 Bioinformatics and Biology Insights  
We extracted background knowledge from MSV3d, a database of all human missense variants mapped to 3D protein structure.  ...  In this study, we identified 8,117 mutations in 805 proteins with known three-dimensional structures that were known to be involved in human monogenic disease.  ...  : authorship and contributorship, conflicts of interest, privacy and confidentiality and (where applicable) protection of human and animal research subjects.  ... 
doi:10.4137/bbi.s11184 pmid:23589683 pmcid:PMC3615990 fatcat:tp7dx3s5ybdnrnptlkhwl6lula

PSnpBind: a database of mutated binding site protein–ligand complexes constructed using a multithreaded virtual screening workflow

Ammar Ammar, Rachel Cavill, Chris Evelo, Egon Willighagen
2022 Journal of Cheminformatics  
It provides a web interface to explore and visualize the protein–ligand complexes and a REST API to programmatically access the different aspects of the database contents.  ...  Thus, a reference dataset of ligands binding affinities to proteins with all their reported binding sites' variants was constructed using a molecular docking approach.  ...  Step 4: Introducing the missense variants to the protein structures After finding the missense variants in the binding pockets of the selected proteins, mutations were introduced to the protein structures  ... 
doi:10.1186/s13321-021-00573-5 pmid:35227289 pmcid:PMC8886843 fatcat:mac7atc7kzb4hk7lbimzzkd5z4

Single amino acid polymorphism in aldehyde dehydrogenase gene superfamily

C. George Priya Doss
2015 Frontiers in Bioscience  
SAPs of all human proteins and the 3D structure mappings are annotated by MSV3d pipeline (Missense Variant mapped to 3D structure) (121).  ...  TD Luu, AM Rusu, V Walter, R Ripp, L Moulinier, J Muller, T Toursel, JD Thompson, O Poch, H Nguyen: MSV3d: database of human Missense variants mapped to 3D protein structure.  ... 
doi:10.2741/4313 pmid:25553455 fatcat:5mbzzwfkz5h7bftn5so5qtaabq

SDS, a structural disruption score for assessment of missense variant deleteriousness

Thanawadee Preeprem, Greg Gibson
2014 Frontiers in Genetics  
We have developed a novel structure-based evaluation for missense variants that explicitly models protein structure and amino acid properties to predict the likelihood that a variant disrupts protein function  ...  We contrasted the candidate epilepsy variants with scores for likely benign variants found in the EVS database, and for positive control variants in the same genes that are suspected to promote a range  ...  ACKNOWLEDGMENTS This work was supported by start-up funds from the Georgia Tech Research Foundation to Greg Gibson, and Thanawadee Preeprem was supported by the School of Biology at Georgia Tech.  ... 
doi:10.3389/fgene.2014.00082 pmid:24795746 pmcid:PMC4001065 fatcat:b4qefhwtifgyln7m7vhax37xzy

A comprehensive study of small non-frameshift insertions/deletions in proteins and prediction of their phenotypic effects by a machine learning method (KD4i)

Carlos Bermejo-Das-Neves, Hoan-Ngoc Nguyen, Olivier Poch, Julie D Thompson
2014 BMC Bioinformatics  
In particular, many Indels that occur in protein coding regions are known to impact the structure or function of the protein.  ...  A major challenge is to predict the effects of these Indels and to distinguish between deleterious and neutral variants.  ...  Acknowledgements We would like to thank the members of the BISTRO Bioinformatics Platform in Strasbourg for their support.  ... 
doi:10.1186/1471-2105-15-111 pmid:24742296 pmcid:PMC4021375 fatcat:55djrwszhzaz3dfpcomxwf46v4

Disruption of N-linked glycosylation promotes proteasomal degradation of the human ATP-binding cassette transporter ABCA3

Michael F. Beers, Ming Zhao, Yaniv Tomer, Scott J. Russo, Peggy Zhang, Linda W. Gonzales, Susan H. Guttentag, Surafel Mulugeta
2013 American Journal of Physiology - Lung cellular and Molecular Physiology  
Fluorescence imaging of transiently transfected A549 or primary human AT2 cells showed that although single motif mutants exhibited a vesicular distribution pattern similar to wildtype ABCA3, mutation  ...  Disruption of N-linked glycosylation promotes proteasomal degradation of the human ATPbinding cassette transporter ABCA3.  ...  Finally, ABCA3 sequence variants carrying a N124S (rs142977595) or N140H (rs45447801) substitution naturally occur in the human population [Human Amino Acid Missense Variant Server Database (humsavar)  ... 
doi:10.1152/ajplung.00184.2013 pmid:24142515 pmcid:PMC3882536 fatcat:5dxej3e3nbcknczvtntakgoq5a

Genome-Wide Association Study for Circulating Tissue Plasminogen Activator Levels and Functional Follow-Up Implicates Endothelial STXBP5 and STX2

J. Huang, J. E. Huffman, M. Yamakuchi, S. Trompet, F. W. Asselbergs, M. Sabater-Lleal, D.-A. Tregouet, W.-M. Chen, N. L. Smith, M. E. Kleber, S.-Y. Shin, D. M. Becker (+80 others)
2014 Arteriosclerosis, Thrombosis and Vascular Biology  
The online version of the article has been corrected and is available at http://atvb.ahajournals. org/content/34/5/1093.  ...  Acknowledgments We acknowledge the essential role of the Cohorts for Heart and Aging Research in Genome Epidemiology (CHARGE) Consortium in providing a collaboration protocol and data-sharing resource  ...  B to D, Silencing STX2 or STXBP5 decreased the target protein expression in human umbilical vein endothelial cells(HUVECs; B), human aortic endothelial cells (HAEC; C), and human dermal microvascular endothelial  ... 
doi:10.1161/atvbaha.113.302088 pmid:24578379 pmcid:PMC4009733 fatcat:sczeapkwhbbohkqiq3vrh4h6ii

A bioinformatics study of protein folding, aggregation and disease

Chen Li
2017
The objective of this PhD thesis is to provide insightful analyses and biological data resources of protein structural and sequence features that are strongly associated with protein function and disease  ...  Building upon the previously published PolyQ database, an updated database, named PolyQ 2.0, has been constructed by incorporating functional and structural annotations for human disease- and non-disease  ...  His research interests are structural bioinformatics, systems biology, data mining and machine learning.  ... 
doi:10.4225/03/58af7bb751296 fatcat:ahtluzkhwfev7l244b7podmere