15 papers · ranked by Valyu relevance
Kenneth R. Durbin, Matthew T. Robey, Lilien N. Voong, Ryan T. Fellers + 4 more
Defining Protein Complex Composition from Native Top-Down Mass Spectrometry Data Authors: ['Kenneth R. Durbin' 'Matthew T. Robey' 'Lilien N. Voong' 'Ryan T. Fellers' 'Corinne A. Lutomski' 'Tarick J. El-Baba' 'Carol V. Robinson' 'Neil L. Kelleher'] Native mass spectrometry has recently moved alongside traditional…
Joeri van Strien, Felix Evers, Madhurya Lutikurti, Stijn L. Berendsen + 8 more
'Stijn L. Berendsen' 'Alejandro Garanto' 'Geert-Jan van Gemert' 'Alfredo Cabrera-Orefice' 'Richard J. Rodenburg' 'Ulrich Brandt' 'Taco W. A. Kooij' 'Martijn A. Huynen' 'Dina Schneidman'] Complexome profiling allows large-scale, untargeted, and comprehensive characterization of protein complexes in a biological sample…
Sébastien Sueron, Sayyed Jalil Mahdizadeh, Eric Chevet, Xavier Guillory + 2 more
PROteolysis TArgeting Chimeras (PROTACs) are bifunctional molecules designed to induce targeted protein degradation by forming a transient ternary complex between an E3 ubiquitin ligase and a protein of interest (POI), leading to the E3-mediated ubiquitination of the POI and its subsequent proteasomal degradation.…
Hui Peng, Limsoon Wong, Wilson Wen Bin Goh, Arne Elofsson
In mass spectrometry (MS)-based proteomics, protein inference from identified peptides (protein fragments) is a critical step. We present ProInfer (Protein Inference), a novel protein assembly method that takes advantage of information in biological networks. ProInfer assists recovery of proteins supported only by…
Sebastian Deorowicz, Adam Gudyś, Arne Elofsson
We used two large databases of predicted protein structures in the experiments: APSD v4 and ESM Atlas containing 214M and 772M structures, respectively. The testing machine was equipped with a 64-core AMD 3995WX Pro CPU clocked at 2.7 GHz and 512 GiB RAM running under openSUSE Tumbleweed operating system. The disks…
Mesih Kilinc, Kejue Jia, Robert L. Jernigan
Title: Significance Homolog detection, finding similar proteins to an unknown protein, is usually the first step in understanding the role and function of that protein. However, if the identity of protein sequences between query and target proteins is low (< 30%), traditional tools struggle to distinguish a correct…
Yanlin Mi, Stefan-Bogdan Marcu, Sabin Tabirca, Venkata V. B. Yallapragada
'Venkata V. B. Yallapragada'] Introduction: In the field of bioinformatics and computational biology, protein structure modelling and analysis is a crucial aspect. However, most existing tools require a high degree of technical expertise and lack a user-friendly interface. To address this problem, we developed a…
Nathaniel Felbinger, Helder V Ribeiro-Filho, Brian G Pierce
The ability to control protein conformations and dynamics through structure-based design has been useful in various scenarios, including engineering of viral antigens for vaccines. One effective design strategy is the substitution of residues to proline amino acids, which due to its unique cyclic side chain can favor…
Petar Petrov, Valerio Izzi
Background Amino acid sequence characterization is a fundamental part of virtually any protein analysis, and creating concise and clear protein topology schemes is of high importance in proteomics studies. Although numerous databases and prediction servers exist, it is challenging to incorporate data from various, and…
Jürgen Bartel, Philipp T Kaulich, Borja Ferrero-Bordera, Rick Gelhausen + 4 more
In proteome studies, the application of alternative proteases, exclusively or in addition to trypsin, often increases protein sequence or proteome coverage. It has recently been shown that, in particular, the analysis of small proteins benefits from such multi-protease approaches. However, selecting the most optimal…
Krzysztof Mularski, Dawid Makalowski, Marcin Okonek, Daria Glebowska + 6 more
'Mateusz Swiercz' 'Karol Kamel' 'Jacek Blazewicz' 'Maciej Antczak' 'Aleksandra Swiercz' 'Soumendranath Bhakat'] The main goal of Molecular Dynamics (MD) is a simulation of a physical system motions in a fixed time period. This technique allows users to observe the dynamic evolution of the system but requires advanced…
Germán Meléndrez Carballo, Karen Guerrero Vázquez, Luis A. García-González, Gabriel Del Rio + 3 more
'Luis A. García-González' 'Gabriel Del Rio' 'Carlos A. Brizuela' 'Jean-Marc Sabatier' 'Marc Maresca'] Antimicrobial peptides (AMPs) have gained the attention of the research community for being an alternative to conventional antimicrobials to fight antibiotic resistance and for displaying other pharmacologically…
Shivani V. Pawar, Wilson Sena Kwaku Banini, Musa Muhammad Shamsuddeen, Toheeb A. Jumah + 3 more
'Toheeb A. Jumah' 'Nigel N. O. Dolling' 'Abdulwasiu Tiamiyu' 'Olaitan I. Awe'] Introduction Homology modeling is a widely used computational technique for predicting the three-dimensional (3D) structures of proteins based on known templates,evolutionary relationships to provide structural insights critical for…
Jiancheng Zhong, Yicheng Luo, Chen Yang, Maoqi Yuan + 1 more
In top-down proteomics, the accurate identification and characterization of proteoform through mass spectrometry represents a critical objective. As a result, achieving accuracy in identification results is essential. Multiple primary structure alterations in proteins generate a diverse range of proteoforms, resulting…
E.H. Bowler-Barnett, J. Fan, J. Luo, M. Magrane + 2 more
'S. Orchard' ''] The human proteome comprises of all of the proteins produced by the sequences translated from the human genome with additional modifications in both sequence and function caused by nonsynonymous variants and posttranslational modifications including cleavage of the initial transcript into smaller…