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WALTZ-DB 2.0: an updated database containing structural information of experimentally determined amyloid-forming peptides

2019 Nucleic Acids Research  
Here, we describe WALTZ-DB 2.0, an updated and significantly expanded open-access database providing information on experimentally determined amyloid-forming hexapeptide sequences (http://waltzdb.switchlab.org  ...  We have updated WALTZ-DB 2.0 with new entries, including: (i) experimental validation of an in-house developed dataset of 229 hexapeptides, using electron microscopy and Thioflavin-T binding assays; (ii  ...  Following this demand, here we describe the fully updated and significantly expanded WALTZ-DB 2.0, the largest publicly available repository for experimentally determined amyloid-forming peptide sequences  ... 
doi:10.1093/nar/gkz758 pmid:31504823 pmcid:PMC6943037 fatcat:dacxy442xndapcu3hl72nyqky4

Structure-based machine-guided mapping of amyloid sequence space reveals uncharted sequence clusters with higher solubilities

Nikolaos Louros, Gabriele Orlando, Matthias De Vleeschouwer, Frederic Rousseau, Joost Schymkowitz
2020 Nature Communications  
Here, we took advantage of the increasing amount of high-resolution structural information on amyloid cores currently available in the protein databank to implement a machine learning approach, named Cordax  ...  The currently charted amyloid sequence space is strongly biased towards hydrophobic, beta-sheet prone sequences that form the core of globular proteins and by Q/N/Y rich yeast prions.  ...  For peptide aggregation propensity, we used a dataset of 1402 non-redundant hexapeptides contained in the WALTZ-DB 2.0 repository 32 .  ... 
doi:10.1038/s41467-020-17207-3 pmid:32620861 fatcat:3shzkk6robe47koayk37qggaam

In silico Approaches for the Design and Optimization of Interfering Peptides Against Protein-Protein Interactions

Zahra Sadat Hashemi, Mahboubeh Zarei, Mohsen Karami Fath, Mahmoud Ganji, Mahboube Shahrabi Farahani, Fatemeh Afsharnouri, Navid Pourzardosht, Bahman Khalesi, Abolfazl Jahangiri, Mohammad Reza Rahbar, Saeed Khalili
2021 Frontiers in Molecular Biosciences  
Moreover, different databases and software tools have been created to predict the peptide structures and their interactions with target protein complexes.  ...  High-throughput screening of large peptide libraries against PPIs; "hotspot" identification; structure-based and off-structure approaches of peptide design; 3D peptide modeling; peptide optimization strategies  ...  ACKNOWLEDGMENTS The authors wish to thank Shahid Rajaee Teacher Training University for supporting the conduct of this research.  ... 
doi:10.3389/fmolb.2021.669431 pmid:33996914 pmcid:PMC8113820 fatcat:j2ie7erd3rcfbfrnlh3yvzzm3q

A bioinformatics study of protein folding, aggregation and disease

Chen Li
2017
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  ...  CCD is a type of protein tertiary structure consisting of an ensemble of helices binding together. It has been estimated that approximately 10% of eukaryotic proteins contain CCDs.  ...  His research interests are structural bioinformatics, systems biology, data mining and machine learning.  ... 
doi:10.4225/03/58af7bb751296 fatcat:ahtluzkhwfev7l244b7podmere

International Academy of Cardiology Annual Scientific Sessions 2018

2018 Cardiology  
any information storage and retrieval system, without permission in writing from the publisher or, in the case of photocopying, direct payment of a specifi ed fee to the Copyright Clearance Center (see  ...  No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, microcopying, or by  ...  Indication of revascularization of 2 or 3 major coronary arteries and/or unprotected left main (ULMD) was an inclusion criteria in ERACI IV but not in WALTZ, an all-comers registry, including STEMI.  ... 
doi:10.1159/000491714 fatcat:nehdnfpnhzbzfmcbfo4op2sjji

Abstracts

2002 Journal of Cystic Fibrosis  
This review will concentrate on those therapeutic strategies founded on our growing knowledge of the molecular basis of CF. These may be divided into four categories.  ...  Only five strains contained an erm gene and two an msr(A) gene.Nucleotide sequence of ribosomal structures forming the binding site of erythromycin, ribosomal proteins L4 and L22, and 23S rRNA (domains  ...  This is the first example of a structurally known mini-chromosome made to contain an active therapeutic gene. UDCA is discontinued if these parameters are normal for more than 12 months.  ... 
doi:10.1016/s1569-1993(02)00030-9 fatcat:w4ou7htgh5afppud2v4tnz5dzy

• Oral Presentations • A-002 Experiences of discrimination in a sample of LG-BTT people in Puerto Rico

Abstracts, Prhsj
2014 unpublished
SRY contains a high mobility group (HMG) box domain, required for specific DNA binding The structure of the HMG box domain contains three α-helices, separated by loops, a strucconserved domain among an  ...  Although 10% were found to contain exonic sequence of a gene, none of them was present in the database of known ATXN1 interac-tors.  ...  After depletion ,100 µg of proteins were analyzed by SDS-PAGE. After in-gel digestion, peptides from HIV+ cocaine-were labeled with 16O and peptides from HIV+ cocaine + were labeled with 18O.  ... 
fatcat:kin6twg2ubchfjao27zsrdq4my