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A sequence-based evolutionary distance method for Phylogenetic analysis of highly divergent proteins
- Wei Cao
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Characterization of signal and transit peptides based on motif composition and taxon-specific patterns
- Katarzyna Sidorczuk
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Genome-wide analysis and characterization of the LRR-RLK gene family provides insights into anthracnose resistance in common bean
- Caroline Marcela da Silva Dambroz
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Unveiling the functional epitopes of cobra venom cytotoxin by immunoinformatics and epitope-omic analyses
- Jia Jin Hiu
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Full-scale network analysis reveals properties of the FV protein structure organization
- André J. Ferreira-Martins
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A strategy for evaluating potential antiviral resistance to small molecule drugs and application to SARS-CoV-2
- Karen Sargsyan
- , Karine Mazmanian
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Pan-kinome of Legionella expanded by a bioinformatics survey
- Marianna Krysińska
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- & Marcin Gradowski
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Massive annotation of bacterial l-asparaginases reveals their puzzling distribution and frequent gene transfer events
- Andrzej Zielezinski
- , Joanna I. Loch
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Deep embeddings to comprehend and visualize microbiome protein space
- Krzysztof Odrzywolek
- , Zuzanna Karwowska
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Substantiation of propitious “Enzybiotic” from two novel bacteriophages isolated from a wastewater treatment plant in Qatar
- Ramya Ramadoss
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- & Annette Shoba Vincent
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A computational method for predicting nucleocapsid protein in retroviruses
- Manyun Guo
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Protein embeddings and deep learning predict binding residues for various ligand classes
- Maria Littmann
- , Michael Heinzinger
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Computational identification of multiple lysine PTM sites by analyzing the instance hardness and feature importance
- Sabit Ahmed
- , Afrida Rahman
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Analysis of the dark proteome of Chandipura virus reveals maximum propensity for intrinsic disorder in phosphoprotein
- Nishi R. Sharma
- , Kundlik Gadhave
- & Rajanish Giri
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Natural variants in SARS-CoV-2 Spike protein pinpoint structural and functional hotspots with implications for prophylaxis and therapeutic strategies
- Suman Pokhrel
- , Benjamin R. Kraemer
- & Daria Mochly-Rosen
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Master Blaster: an approach to sensitive identification of remotely related proteins
- Chintalapati Janaki
- , Venkatraman S. Gowri
- & Narayanaswamy Srinivasan
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Coevolution underlies GPCR-G protein selectivity and functionality
- Min Jae Seo
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- & Wookyung Yu
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In silico detection of SARS-CoV-2 specific B-cell epitopes and validation in ELISA for serological diagnosis of COVID-19
- Isabelle Q. Phan
- , Sandhya Subramanian
- & Wesley C. Van Voorhis
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Intrinsic disorder in protein domains contributes to both organism complexity and clade-specific functions
- Chao Gao
- , Chong Ma
- & Dong Yang
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Characterization and identification of lysine crotonylation sites based on machine learning method on both plant and mammalian
- Rulan Wang
- , Zhuo Wang
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Epitope similarity cannot explain the pre-formed T cell immunity towards structural SARS-CoV-2 proteins
- Ulrik Stervbo
- , Sven Rahmann
- & Nina Babel
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Distribution of disease-causing germline mutations in coiled-coils implies an important role of their N-terminal region
- Zsofia E. Kalman
- , Bálint Mészáros
- & Laszlo Dobson
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Machine learning-guided discovery and design of non-hemolytic peptides
- Fabien Plisson
- , Obed Ramírez-Sánchez
- & Cristina Martínez-Hernández
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Identification of novel molecular determinants of co-receptor usage in HIV-1 subtype F V3 envelope sequences
- Maximiliano Distefano
- , Esteban Lanzarotti
- & Paula Aulicino
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Structural basis for substrate and product recognition in human phosphoglucomutase-1 (PGM1) isoform 2, a member of the α-d-phosphohexomutase superfamily
- Paul Hoff Backe
- , Jon K. Laerdahl
- & Magnar Bjørås
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Computational modelling of wet adhesive mussel foot proteins (Bivalvia): Insights into the evolutionary convolution in diverse perspectives
- P. P. Anand
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Deep Analysis of Residue Constraints (DARC): identifying determinants of protein functional specificity
- Farzaneh Tondnevis
- , Elizabeth E. Dudenhausen
- & Andrew F. Neuwald
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Exploring the limitations of biophysical propensity scales coupled with machine learning for protein sequence analysis
- Daniele Raimondi
- , Gabriele Orlando
- & Yves Moreau
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Amino acid substitution scoring matrices specific to intrinsically disordered regions in proteins
- Rakesh Trivedi
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Deeper Profiles and Cascaded Recurrent and Convolutional Neural Networks for state-of-the-art Protein Secondary Structure Prediction
- Mirko Torrisi
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Structure-based identification of a potential non-catalytic binding site for rational drug design in the fructose 1,6-biphosphate aldolase from Giardia lamblia
- Sara-Teresa Méndez
- , Adriana Castillo-Villanueva
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Stoichiogenomics reveal oxygen usage bias, key proteins and pathways associated with stomach cancer
- Xiaoyan Zuo
- , Bo Li
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Compensated pathogenic variants in coagulation factors VIII and IX present complex mapping between molecular impact and hemophilia severity
- Òscar Marín
- , Josu Aguirre
- & Xavier de la Cruz
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Α Quantum Pattern Recognition Method for Improving Pairwise Sequence Alignment
- Konstantinos Prousalis
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Identification of non-specific Lipid Transfer Protein gene family members in Solanum lycopersicum and insights into the features of Sola l 3 protein
- Nunzio D’Agostino
- , Martina Buonanno
- & Maria Manuela Rigano
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PhoglyStruct: Prediction of phosphoglycerylated lysine residues using structural properties of amino acids
- Abel Chandra
- , Alok Sharma
- & Tatsuhiko Tsunoda
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Reconstructing the evolutionary history of F420-dependent dehydrogenases
- M. Laura Mascotti
- , Hemant Kumar
- & Marco W. Fraaije
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Large-scale in-silico statistical mutagenesis analysis sheds light on the deleteriousness landscape of the human proteome
- Daniele Raimondi
- , Gabriele Orlando
- & Wim F. Vranken
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Proteomics reveals ablation of PlGF increases antioxidant and neuroprotective proteins in the diabetic mouse retina
- Madhu Sudhana Saddala
- , Anton Lennikov
- & Hu Huang
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Global pentapeptide statistics are far away from expected distributions
- Jarosław Poznański
- , Jan Topiński
- & Marcin Grynberg
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Pattern to Knowledge: Deep Knowledge-Directed Machine Learning for Residue-Residue Interaction Prediction
- Andrew K. C. Wong
- , Ho Yin Sze-To
- & Gary L. Johanning
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Predictions of novel Schistosoma mansoni - human protein interactions consistent with experimental data
- J. White Bear
- , Thavy Long
- & James H. McKerrow
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IDPpi: Protein-Protein Interaction Analyses of Human Intrinsically Disordered Proteins
- Vladimir Perovic
- , Neven Sumonja
- & Nevena Veljkovic
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Structural basis for cross-reactivity and conformation fluctuation of the major beech pollen allergen Fag s 1
- Adolfo H. Moraes
- , Claudia Asam
- & Ana Paula Valente
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Assigning biological function using hidden signatures in cystine-stabilized peptide sequences
- S. M. Ashiqul Islam
- , Christopher Michel Kearney
- & Erich J. Baker
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Investigation of immunogenic properties of Hemolin from silkworm, Bombyx mori as carrier protein: an immunoinformatic approach
- Veeranarayanan Surya Aathmanathan
- , Nattarsingam Jothi
- & Muthukalingan Krishnan
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Evolutionary convergence and divergence in archaeal chromosomal proteins and Chromo-like domains from bacteria and eukaryotes
- Gurmeet Kaur
- , Lakshminarayan M. Iyer
- & L. Aravind
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Aminode: Identification of Evolutionary Constraints in the Human Proteome
- Kevin T. Chang
- , Junyan Guo
- & Marco Sardiello
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Random protein sequences can form defined secondary structures and are well-tolerated in vivo
- Vyacheslav Tretyachenko
- , Jiří Vymětal
- & Klára Hlouchová
Prediction of linear B-cell epitopes based on protein sequence features and BERT embeddings