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| Open AccessIdentification of domains in Plasmodium falciparum proteins of unknown function using DALI search on AlphaFold predictions
- Hannah Michaela Behrens
- & Tobias Spielmann
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| Open AccessDeepReg: a deep learning hybrid model for predicting transcription factors in eukaryotic and prokaryotic genomes
- Leonardo Ledesma-Dominguez
- , Erik Carbajal-Degante
- & Ernesto Perez-Rueda
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| Open AccessCCDC58 is a potential biomarker for diagnosis, prognosis, immunity, and genomic heterogeneity in pan-cancer
- Kai Yang
- , Yan Ma
- & Ruohan Zhang
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| Open AccessCharacterization of a putative orexin receptor in Ciona intestinalis sheds light on the evolution of the orexin/hypocretin system in chordates
- Maiju K. Rinne
- , Lauri Urvas
- & Henri Xhaard
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| Open AccessVirtuousPocketome: a computational tool for screening protein–ligand complexes to identify similar binding sites
- Lorenzo Pallante
- , Marco Cannariato
- & Marco A. Deriu
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| Open AccessCharacterizing conformational states in GPCR structures using machine learning
- Ilya Buyanov
- & Petr Popov
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| Open AccessA repertoire of candidate effector proteins of the fungus Ceratocystis cacaofunesta
- Gabriela N. Ramos-Lizardo
- , Jonathan J. Mucherino-Muñoz
- & Ronan Xavier Corrêa
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| Open AccessAiKPro: deep learning model for kinome-wide bioactivity profiling using structure-based sequence alignments and molecular 3D conformer ensemble descriptors
- Hyejin Park
- , Sujeong Hong
- & Jae-Min Shin
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| Open AccessRare variant contribution to cholestatic liver disease in a South Asian population in the United Kingdom
- Julia Zöllner
- , Sarah Finer
- & Peter H. Dixon
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Article
| Open AccessCoenzyme A binding sites induce proximal acylation across protein families
- Chris Carrico
- , Andrew Cruz
- & Eric Verdin
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| Open AccessAccurate prediction by AlphaFold2 for ligand binding in a reductive dehalogenase and implications for PFAS (per- and polyfluoroalkyl substance) biodegradation
- Hao-Bo Guo
- , Vanessa A. Varaljay
- & Rajiv Berry
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| Open AccessOptimizing variant-specific therapeutic SARS-CoV-2 decoys using deep-learning-guided molecular dynamics simulations
- Katharina Köchl
- , Tobias Schopper
- & Christian C. Gruber
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| Open AccessPan-kinome of Legionella expanded by a bioinformatics survey
- Marianna Krysińska
- , Bartosz Baranowski
- & Marcin Gradowski
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Article
| Open AccessStructural informatic study of determined and AlphaFold2 predicted molecular structures of 13 human solute carrier transporters and their water-soluble QTY variants
- Eva Smorodina
- , Igor Diankin
- & Shuguang Zhang
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| Open AccessThe effect of mutations on binding interactions between the SARS-CoV-2 receptor binding domain and neutralizing antibodies B38 and CB6
- Jonathan E. Barnes
- , Peik K. Lund-Andersen
- & F. Marty Ytreberg
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| Open AccessParallel functional annotation of cancer-associated missense mutations in histone methyltransferases
- Ashley J. Canning
- , Susan Viggiano
- & Michael S. Cosgrove
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Article
| Open AccessImproving protein succinylation sites prediction using embeddings from protein language model
- Suresh Pokharel
- , Pawel Pratyush
- & Dukka B. KC
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Article
| Open AccessDe novo metatranscriptomic exploration of gene function in the millipede holobiont
- Puspendu Sardar
- , Vladimír Šustr
- & Lucie Faktorová
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Article
| Open AccessProteinGLUE multi-task benchmark suite for self-supervised protein modeling
- Henriette Capel
- , Robin Weiler
- & K. Anton Feenstra
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Article
| Open AccessIdentification and expression of functionally conserved circadian clock genes in lichen-forming fungi
- Henrique F. Valim
- , Francesco Dal Grande
- & Imke Schmitt
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Article
| Open AccessExploring the medicinally important secondary metabolites landscape through the lens of transcriptome data in fenugreek (Trigonella foenum graecum L.)
- Mahantesha B. N. Naika
- , Nitish Sathyanarayanan
- & Ramanathan Sowdhamini
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Article
| Open AccessGene function prediction in five model eukaryotes exclusively based on gene relative location through machine learning
- Flavio Pazos Obregón
- , Diego Silvera
- & Rafael Cantera
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| Open AccessAlphaFold2 models indicate that protein sequence determines both structure and dynamics
- Hao-Bo Guo
- , Alexander Perminov
- & Rajiv Berry
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Article
| Open AccessMulti-task learning to leverage partially annotated data for PPI interface prediction
- Henriette Capel
- , K. Anton Feenstra
- & Sanne Abeln
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Article
| Open AccessA novel method for assessing and measuring homophily in networks through second-order statistics
- Nicola Apollonio
- , Paolo G. Franciosa
- & Daniele Santoni
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| Open AccessDynamic insights into the effects of nonsynonymous polymorphisms (nsSNPs) on loss of TREM2 function
- Raju Dash
- , Yeasmin Akter Munni
- & Il Soo Moon
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| Open AccessNon-covalent Fc-Fab interactions significantly alter internal dynamics of an IgG1 antibody
- Ramakrishnan Natesan
- & Neeraj J. Agrawal
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| Open AccessLM-GVP: an extensible sequence and structure informed deep learning framework for protein property prediction
- Zichen Wang
- , Steven A. Combs
- & Peter M. Clark
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| Open AccessLIM domain-wide comprehensive virtual mutagenesis provides structural rationale for cardiomyopathy mutations in CSRP3
- Pankaj Kumar Chauhan
- & Ramanathan Sowdhamini
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| Open AccessInteractions of Co, Cu, and non-metal phthalocyanines with external structures of SARS-CoV-2 using docking and molecular dynamics
- Wilson Luna Machado Alencar
- , Tiago da Silva Arouche
- & Antonio Maia de Jesus Chaves Neto
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| Open AccessA deep learning model to detect novel pore-forming proteins
- Theju Jacob
- & Theodore W. Kahn
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Article
| Open AccessExtracting phylogenetic dimensions of coevolution reveals hidden functional signals
- Alexandre Colavin
- , Esha Atolia
- & Kerwyn Casey Huang
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Article
| Open AccessIn-silico phenotype prediction by normal mode variant analysis in TUBB4A-related disease
- Avi Fellner
- , Yael Goldberg
- & Felix Benninger
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| Open AccessProtein embeddings and deep learning predict binding residues for various ligand classes
- Maria Littmann
- , Michael Heinzinger
- & Burkhard Rost
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| Open AccessACP-MHCNN: an accurate multi-headed deep-convolutional neural network to predict anticancer peptides
- Sajid Ahmed
- , Rafsanjani Muhammod
- & Abdollah Dehzangi
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| Open AccessApoplastic effector candidates of a foliar forest pathogen trigger cell death in host and non-host plants
- Lukas Hunziker
- , Mariana Tarallo
- & Rosie E. Bradshaw
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Article
| Open AccessAutoencoder-based detection of the residues involved in G protein-coupled receptor signaling
- Yuko Tsuchiya
- , Kei Taneishi
- & Yasushige Yonezawa
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| Open AccessTheoretical and experimental study of interaction of macroheterocyclic compounds with ORF3a of SARS-CoV-2
- Natalia Sh. Lebedeva
- , Yury A. Gubarev
- & Oskar I. Koifman
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Article
| Open AccessComputational identification of multiple lysine PTM sites by analyzing the instance hardness and feature importance
- Sabit Ahmed
- , Afrida Rahman
- & S. M. Shovan
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| Open AccessInsights into the substrate binding mechanism of SULT1A1 through molecular dynamics with excited normal modes simulations
- Balint Dudas
- , Daniel Toth
- & Maria A. Miteva
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| Open AccessA deep learning based approach for prediction of Chlamydomonas reinhardtii phosphorylation sites
- Niraj Thapa
- , Meenal Chaudhari
- & Dukka B. KC
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| Open AccessCritical assessment of coiled-coil predictions based on protein structure data
- Dominic Simm
- , Klas Hatje
- & Martin Kollmar
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| Open AccessPredicting MHC I restricted T cell epitopes in mice with NAP-CNB, a novel online tool
- Carlos Wert-Carvajal
- , Rubén Sánchez-García
- & Arrate Muñoz-Barrutia
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| Open AccessDifference of binding modes among three ligands to a receptor mSin3B corresponding to their inhibitory activities
- Tomonori Hayami
- , Narutoshi Kamiya
- & Junichi Higo
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| Open AccessAn in silico deep learning approach to multi-epitope vaccine design: a SARS-CoV-2 case study
- Zikun Yang
- , Paul Bogdan
- & Shahin Nazarian
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| Open AccessImproved prediction and characterization of anticancer activities of peptides using a novel flexible scoring card method
- Phasit Charoenkwan
- , Wararat Chiangjong
- & Watshara Shoombuatong
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| Open AccessComparative transcriptomics and host-specific parasite gene expression profiles inform on drivers of proliferative kidney disease
- Marc Faber
- , Sophie Shaw
- & Jason W. Holland
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| Open AccessEmbeddings from deep learning transfer GO annotations beyond homology
- Maria Littmann
- , Michael Heinzinger
- & Burkhard Rost
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| Open AccessIn silico analysis of epitope-based vaccine candidate against tuberculosis using reverse vaccinology
- Shaheen Bibi
- , Inayat Ullah
- & Shiquan Niu