15 papers · ranked by Valyu relevance
S. Srivastava, S. B. Lal, D. C. Mishra, U. B. Angadi + 3 more
The proposed algorithm has been implemented in R software. In order to evaluate the performance of the proposed algorithm for protein 3D structure comparison with existing algorithms i.e., (1) CE, (2) jFATCAT and (3) ESA, the benchmark data was collected from the literature . Further, distance matrices based on all…
Daniel Barthel, Jonathan D Hirst, Jacek Błażewicz, Edmund K Burke + 1 more
'Natalio Krasnogor'] Background We introduce the decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information (ProCKSI). ProCKSI integrates various protein similarity measures through an easy to use interface that allows the comparison of multiple proteins simultaneously. It employs…
Carol J Bult, Harold J Drabkin, Alexei Evsikov, Darren Natale + 7 more
'Cecilia Arighi' 'Natalia Roberts' 'Alan Ruttenberg' "Peter D'Eustachio" 'Barry Smith' 'Judith A Blake' 'Cathy Wu'] Background Representing species-specific proteins and protein complexes in ontologies that are both human- and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data…
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…
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…
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…
Noam Kaplan, Moriah Friedlich, Menachem Fromer, Michal Linial
Background It is a major challenge of computational biology to provide a comprehensive functional classification of all known proteins. Most existing methods seek recurrent patterns in known proteins based on manually-validated alignments of known protein families. Such methods can achieve high sensitivity, but are…
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…
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…
Alejandro Real-Chicharro, Iván Ruiz-Mostazo, Ismael Navas-Delgado, Amine Kerzazi + 4 more
'Amine Kerzazi' 'Othmane Chniber' 'Francisca Sánchez-Jiménez' 'Miguel Ángel Medina' 'José F Aldana-Montes'] Background Protein-protein interactions can be considered the basic skeleton for living organism self-organization and homeostasis. Impressive quantities of experimental data are being obtained and computational…
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…
Ken Pendarvis, Ranjit Kumar, Shane C Burgess, Bindu Nanduri
Background Mass spectrometry-based protein identification methods are fundamental to proteomics. Biological experiments are usually performed in replicates and proteomic analyses generate huge datasets which need to be integrated and quantitatively analyzed. The Sequest™ search algorithm is a commonly used algorithm…