Computational and Structural Biotechnology Journal

Article	Citations
Streptomyces coelicolor macrodomain hydrolase SCO6735 cleaves thymidine-linked ADP-ribosylation of DNA	226
An integrated protein structure fitness scoring approach for identifying native-like model structures	213
NGS allele counts versus called genotypes for testing genetic association	166
The second intracellular loop of the yeast Trk1 potassium transporter is involved in regulation of activity, and interaction with 14–3-3 proteins	143
Integrated metabolomics and network analysis reveal changes in lipid metabolisms of tripterygium glycosides tablets in rats with collagen-induced arthritis	134
Identification and biophysical characterization of epitope atlas of Porcine Reproductive and Respiratory Syndrome Virus	130
WUREN: Whole-modal union representation for epitope prediction	118
Corrigendum to “Cryo-EM reveals architectural diversity in active rotavirus particles” [Comput. Struct. Biotechnol. J. 17 (2019) 1178–1183]	106
EthnoHERBS: Harnessing traditional herbal knowledge for biodiversity conservation and innovative health solutions	102
Nextcast: A software suite to analyse and model toxicogenomics data	94
Comprehensive exploration of JQ1 and GSK2801 targets in breast cancer using network pharmacology and molecular modeling approaches	88
Agreement and disagreement in pediatric functional neurological symptom disorders: Comparing patient reported outcome measures (PROMs) and clinician assessments	83
Predicting zeta potential of liposomes from their structure: A nano-QSPR model for DOPE, DC-Chol, DOTAP, and EPC formulations	72
A drug repurposing method based on inhibition effect on gene regulatory network	72
In silico and in vitro approaches allow the identification of the Prosystemin molecular network	72
Network-based prioritization of cancer biomarkers by phenotype-driven module detection and ranking	68
cPEPmatch Webserver: A comprehensive tool and database to aid rational design of cyclic peptides for drug discovery	62
Artificial intelligence predictive system of individual survival rate for lung adenocarcinoma	59
Optimizing the Illumina COVIDSeq laboratorial and bioinformatics pipeline on thousands of samples for SARS-CoV-2 Variants of Concern tracking	59
Consistencies and contradictions in different polymer models of chromatin architecture	59
Entropy-extreme model for predicting the development of cyber epidemics at early stages	58
MUG: A mutation overview of GPCR subfamily A17 receptors	57
Predicting cellular adaptation proteins dependent on eIF2α regulation under stress conditions: physiological and pathophysiological implications in neuronal function	56
Advanced biokinetic and hydrodynamic modelling to support and optimize the design of full-scale high rate algal ponds	56
DIPAN: Detecting personalized intronic polyadenylation derived neoantigens from RNA sequencing data	55

MMRT: MultiMut Recursive Tree for predicting functional effects of high-order protein variants from low-order variants	55
Deep5mC: Predicting 5-methylcytosine (5mC) methylation status using a deep learning transformer approach	55
Structural elucidation of four fungal hydrophobins belonging to classes I and II: Results from Alphafold and accelerated molecular dynamics simulations	53
Altered heme metabolism and hemoglobin concentration due to empirical antibiotics-induced gut dysbiosis in preterm infants	51
Phylogenetic tree-based amino acid sequence generation for proteomics data analysis of unknown species	50
Evolution is in the details: Regulatory differences in modern human and Neanderthal	49
Discovery of a novel marine Bacteroidetes with a rich repertoire of carbohydrate-active enzymes	48
Ranking pre-trained speech embeddings in Parkinson's disease detection: Does Wav2Vec 2.0 outperform its 1.0 version across speech modes and languages?	48
DiabetesOmic: A comprehensive multi-omics diabetes database	48
Free energy landscape of the PI3Kα C-terminal activation	46
Automated machine learning in nanotoxicity assessment: A comparative study of predictive model performance	46
Data pre-processing for analyzing microbiome data – A mini review	46
Towards accurate and efficient diagnoses in nephropathology: An AI-based approach for assessing kidney transplant rejection	45
What remains from living cells in bacterial lysate-based cell-free systems	45
Computation-aided studies related to the induction of specialized metabolite biosynthesis in microbial co-cultures: An introductory overview	44
Biomarker discovery process at binomial decision point (2BDP): Analytical pipeline to construct biomarker panel	44
Improved inter-residue contact prediction via a hybrid generative model and dynamic loss function	44
The balance between photosynthesis and respiration explains the niche differentiation between Crocosphaera and Cyanothece	44
Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects	44
dsCellNet: A new computational tool to infer cell–cell communication networks in the developing and aging brain	43
Identification of (Z)-2-benzylidene-dihydroimidazothiazolone derivatives as tyrosinase inhibitors: Anti-melanogenic effects and in silico studies	42
Predictive dynamic control accurately maps the design space for 2,3-butanediol production	41
UPIMAPI, reCOGnizer and KEGGCharter: Bioinformatics tools for functional annotation and visualization of (meta)-omics datasets	41
Multi-omics landscape and clinical significance of a SMAD4-driven immune signature: Implications for risk stratification and frontline therapies in pancreatic cancer	41
Cell segmentation and representation with shape priors	40
VTAM: A robust pipeline for validating metabarcoding data using controls	40
Towards predicting implant-induced fibrosis: A standardized network model of macrophage-fibroblast interactions	39
From sequence to function through structure: Deep learning for protein design	39
Prediction of protein-ligand binding affinity with deep learning	38
Using molecular dynamics simulations to interrogate T cell receptor non-equilibrium kinetics	38
Statistical methods for Mendelian randomization in genome-wide association studies: A review	37
Design rules applied to silver nanoparticles synthesis: A practical example of machine learning application.	37
A novel exosome-derived prognostic signature and risk stratification for breast cancer based on multi-omics and systematic biological heterogeneity	37
NaCTR: Natural product-derived compound-based drug discovery pipeline from traditional oriental medicine by search space reduction	36
Cat-E: A comprehensive web tool for exploring cancer targeting strategies	35
Pleiotropic expression quantitative trait loci are enriched in enhancers and transcription factor binding sites and impact more genes	35
Contagious infection-free medical interaction system with machine vision controlled by remote hand gesture during an operation	35
Identification of genetic basis of brain imaging by group sparse multi-task learning leveraging summary statistics	35
PLO3S: Protein LOcal Surficial Similarity Screening	35
Inference of essential genes in Brugia malayi and Onchocerca volvulus by machine learning and the implications for discovering new interventions	35
ECGA: A web server to explore and analyze extrachromosomal gene in cancer	34
PS-GO parametric protein search engine	34
Scale bar of aging trajectories for screening personal rejuvenation treatments	34
Prognostic iron-metabolism signature robustly stratifies single-cell characteristics of hepatocellular carcinoma	33
Computationally derived structural insights into Rare Earth selectivity in lanmodulin and its variants	33
Over time analysis of the codon usage of SARS-CoV-2 and its variants	33
Protein design accelerates the development and application of optogenetic tools	33
Bacillus subtilis spores displaying RBD domain of SARS-CoV-2 spike protein	32
YTLR: Extracting yeast transcription factor-gene associations from the literature using automated literature readers	32
Strengths and limitations of web servers for the modeling of TCRpMHC complexes	32

Mutation density analyses on long noncoding RNA reveal comparable patterns to protein-coding RNA and prognostic value	32
Survival estimation in patients with stomach and esophageal carcinoma using miRNA expression profiles	31
Identifying novel SMYD3 interactors on the trail of cancer hallmarks	31
Literature-based translation from synthetic lethality screening into therapeutics targets: CD82 is a novel target for KRAS mutation in colon cancer	31
Performance of a HER2 testing algorithm tailored for urothelial bladder cancer: A Bi-centre study	31
Multicopper oxidases with laccase-ferroxidase activity: Classification and study of ferroxidase activity determinants in a member from Heterobasidion annosum s. l.	31
Computational approaches in rheumatic diseases – Deciphering complex spatio-temporal cell interactions	31
The World of GPCR dimers – Mapping dopamine receptor D2 homodimers in different activation states and configuration arrangements	31
Impact of an irreversible β-galactosylceramidase inhibitor on the lipid profile of zebrafish embryos	31
Dual guide RNA-mediated concurrent C&G-to-T&A and A&T-to-G&C conversions using CRISPR base editors	31
Genome-scale models as a vehicle for knowledge transfer from microbial to mammalian cell systems	31
SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability	30
Review of protein structure-based analyses that illuminate plant stress mechanisms	30
Drug repurposing in psoriasis, performed by reversal of disease-associated gene expression profiles	30
Prediction of HER2-positive breast cancer recurrence and metastasis risk from histopathological images and clinical information via multimodal deep learning	29
A cellulose-degrading Bacillus altitudinis from Tibetan pigs improved the in vitro fermentation characteristics of wheat bran	29
Machine learning in metastatic cancer research: Potentials, possibilities, and prospects	29
PCLDA: An interpretable cell annotation tool for single-cell RNA-sequencing data based on simple statistical methods	29
Augusta: From RNA‐Seq to gene regulatory networks and Boolean models	29
Population genomic analyses reveal evidence for limited recombination in the superbug Candida auris in nature	29
Co-expression of immune checkpoints in glioblastoma revealed by single-nucleus RNA sequencing and spatial transcriptomics	28
Empirical comparison and recent advances of computational prediction of hormone binding proteins using machine learning methods	28
Beyond the Scalpel: Assessing ChatGPT's potential as an auxiliary intelligent virtual assistant in oral surgery	28
Thresholding Gini variable importance with a single-trained random forest: An empirical Bayes approach	28
Structural studies of protein–nucleic acid complexes: A brief overview of the selected techniques	28
Molecular dynamics analysis of the structural properties of the transglutaminases of Kutzneria albida and Streptomyces mobaraensis	27
Interplay of starch debranching enzyme and its inhibitor is mediated by Redox-Activated SPL transcription factor	27
Homologous cardiac calcium pump regulators phospholamban and sarcolipin adopt distinct oligomeric states in the membrane	27
Corrigendum to “Coupling the endophytic microbiome with the host transcriptome in olive roots” [Comput. Struct. Biotechnol. J. 19 (2021) 4777–4789]	27
MSPJ: Discovering potential biomarkers in small gene expression datasets via ensemble learning	27
Analyzing the human gut mycobiome – A short guide for beginners	27
Ion and water permeation through claudin-10b and claudin-15 paracellular channels	27
Whole-genome analysis of carbapenem-resistant Acinetobacter baumannii from clinical isolates in Southern Thailand	27
Structural insights into apoptotic regulation of human Bfk as a novel Bcl-2 family member	27
Detecting differentially expressed circular RNAs from multiple quantification methods using a generalized linear mixed model	27
Differential prolyl hydroxylation by six Physcomitrella prolyl-4 hydroxylases	27
Reprogramming landscape highlighted by dynamic transcriptomes in therapy-induced neuroendocrine differentiation	26
Corrigendum to “TREAT: Therapeutic RNAs exploration inspired by artificial intelligence technology” [Comput Struct Biotechnol J 20 (2022) 5680–5689]	26
Protposer: The web server that readily proposes protein stabilizing mutations with high PPV	26
PgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics – catching the (un)usual suspects	26
TRRAP-mediated acetylation on Sp1 regulates adult neurogenesis	26
A computational algorithm to assess the physiochemical determinants of T cell receptor dissociation kinetics	26
A novel deep learning method for large-scale analysis of bone marrow adiposity using UK Biobank Dixon MRI data	25
Deep learning of antibody epitopes using positional permutation vectors	25
Alterations in 3D chromatin organization contribute to tumorigenesis of EGFR-amplified glioblastoma	25
Machine learning reveals STAT motifs as predictors for GR-mediated gene repression	25
Generic and queryable data integration schema for transcriptomics and epigenomics studies	25
Mysteries of gene regulation: Promoters are not the sole triggers of gene expression	25
Downregulation of ABLIM3 confers to the metastasis of neuroblastoma via regulating the cell adhesion molecules pathway	25
Concentration-dependent thermodynamic analysis of the partition process of small ligands into proteins	24
Dynamical features of smooth muscle actin pathological mutants: The arginine-257(258)-Cysteine cases	24
Claudin-10b cation channels in tight junction strands: Octameric-interlocked pore barrels constitute paracellular channels with low water permeability	24
scDemultiplex: An iterative beta-binomial model-based method for accurate demultiplexing with hashtag oligos	24
Post-processing enhances protein secondary structure prediction with second order deep learning and embeddings	24
Enhancing glucose level prediction of ICU patients through hierarchical modeling of irregular time-series	24
Structure-based identification of HNF4α agonists: Rosmarinic acid as a promising candidate for NAFLD treatment	24
Fantastic genes and where to find them expressed in CHO	23
Advances in gut microbiota functions in inflammatory bowel disease: Dysbiosis, management, cytotoxicity assessment, and therapeutic perspectives	23
Fine-tuning of conditional Transformers improves in silico enzyme prediction and generation	23
Comparative analysis of amino acid auxotrophies and peptidase profiles in non-dysbiotic and dysbiotic small intestinal microbiomes	23
In-silico proteomic analysis of the role of IL-4 and IL-10 in IVD degeneration: Protein-protein interaction networks for candidate prioritisation	23
EquiRank: Improved protein-protein interface quality estimation using protein language-model-informed equivariant graph neural networks	23
Plasma cell-free extrachromosomal circular DNA is a molecular hallmark of preeclampsia	22
Structure analysis of human gut microbiota associated with single-celled gut protists using Next-Generation Sequencing of 16S and 18S rRNA genes	22
Targeting non-structural proteins of Hepatitis C virus for predicting repurposed drugs using QSAR and machine learning approaches	22
Easy-MODA: Simplifying standardised registration of scientific simulation workflows through MODA template guidelines powered by the Enalos Cloud Platform	22
CNN6mA: Interpretable neural network model based on position-specific CNN and cross-interactive network for 6mA site prediction	22
Optimizing fountain codes for DNA data storage	22
HELLS modulates the stemness of intrahepatic cholangiocarcinoma through promoting senescence-associated secretory phenotype	22
Population-scale genotyping of structural variation in the era of long-read sequencing	22
Evolutionary progression of collective mutations in Omicron sub-lineages towards efficient RBD-hACE2: Allosteric communications between and within viral and human proteins	21
New insights empowered by single-cell sequencing: From neural crest to enteric nervous system	21
Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism	21
INSIGHT: An integrated framework for safe and sustainable chemical and material assessment	21
Short-chain fatty acids reprogram metabolic profiles with the induction of reactive oxygen species production in human colorectal adenocarcinoma cells	21
A DNA-based non-infectious replicon system to study SARS-CoV-2 RNA synthesis	21
Modeling approaches for probing cross-feeding interactions in the human gut microbiome	21
Discovery of C-12 dithiocarbamate andrographolide analogues as inhibitors of SARS-CoV-2 main protease: In vitro and in silico studies	21
SPARC: Structural properties associated with residue constraints	21
Evaluation of the impact of printing and embroidery parameters in the process of obtaining utility comfort sensors used in protective clothing dedicated to premature babies	21

EpiCas-DL: Predicting sgRNA activity for CRISPR-mediated epigenome editing by deep learning	21
Targeted removal of mitochondrial DNA from mouse and human extrachromosomal circular DNA with CRISPR-Cas9	21
The seen and the unseen: Molecular classification and image based-analysis of gastrointestinal cancers	21
The structural integrity of the membrane-embedded bacterial division complex FtsQBL studied with molecular dynamics simulations	21
HIV infection detection using CRISPR/Cas systems: Present and future prospects	21
The discovery of hidden guanylate cyclases (GCs) in the Homo sapiens proteome	21
Role of Bmal1 in mediating the cholinergic system to regulate the behavioral rhythm of nocturnal marine molluscs	21
New targets for the treatment of ulcerative colitis: Gut microbiota and its metabolites	20
CNNSplice: Robust models for splice site prediction using convolutional neural networks	20
Reference-based read clustering improves the de novo genome assembly of microbial strains	20
TOAST: A novel method for identifying topologically associated domains based on graph auto-encoders and clustering	20
Structural and functional mapping of ars gene cluster in Deinococcus indicus DR1	20
Shared and divergent contribution of vitamin A and oxytocin to the aetiology of autism spectrum disorder	20
Detection and prioritization of COVID-19 infected patients from CXR images: Analysis of AI-assisted diagnosis in clinical settings	20
MNNMDA: Predicting human microbe-disease association via a method to minimize matrix nuclear norm	20
Demystifying extrachromosomal DNA circles: Categories, biogenesis, and cancer therapeutics	20
A gap analysis of UK biobank publications reveals SNPs associated with intrinsic subtypes of breast cancer	20
fRNC: Uncovering the dynamic and condition-specific RBP-ncRNA circuits from multi-omics data	20
Binding modes of prothrombin cleavage site sequences to the factor Xa catalytic triad: Insights from atomistic simulations	20
Unitig-centered pan-genome machine learning approach for predicting antibiotic resistance and discovering novel resistance genes in bacterial strains	20
SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants	20
Proteome-wide prediction and analysis of the Cryptosporidium parvum protein–protein interaction network through integrative methods	20
Mechanistic insights into P-glycoprotein ligand transport and inhibition revealed by enhanced molecular dynamics simulations	20
Aggregating amyloid resources: A comprehensive review of databases on amyloid-like aggregation	20
Relative flux trade-offs and optimization of metabolic network functionalities	20
Prediction and validation of host-pathogen interactions by a versatile inference approach using Aspergillus fumigatus as a case study	20
Histone variants and chromatin structure, update of advances	20
MM-DRPNet: A multimodal dynamic radial partitioning network for enhanced protein–ligand binding affinity prediction	19
Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop Populus	19
Improving doublet cell removal efficiency through multiple algorithm runs	19
RNA secondary structure prediction by conducting multi-class classifications	19
Identifying the risk of Kawasaki disease based solely on routine blood test features through novel construction of machine learning models	19
Noninvasive detection and interpretation of gastrointestinal diseases by collaborative serum metabolite and magnetically controlled capsule endoscopy	19
MACRAMÉ – Advanced characterisation methodologies to assess and predict the health and environmental risks of advanced materials	19
Cluster parameter-based DBSCAN maps for image characterization	19
Tevenvirinae phages encode a family of LSm-like fold proteins	19
Intraline genomic heterogeneity of the triple-negative breast cancer MDA-MB-231-luc-GFP cell line	19
Data recovery methods for DNA storage based on fountain codes	19
SpatialPPIv2: Enhancing protein–protein interaction prediction through graph neural networks with protein language models	19
Metabolomic and lipidomic insights into the impact of Euglena gracilis-derived β-glucan supplementation on sow colostrum and milk composition	19
Deep learning based deconvolution methods: A systematic review	19
Artificial intelligence-large language models (AI-LLMs) for reliable and accurate cardiotocography (CTG) interpretation in obstetric practice	19
Quercetin: A promising drug candidate against the potential SARS-CoV-2-Spike mutants with high viral infectivity	18
Design, proof-of-concept of single robotic hair transplant mechanisms for both harvest and implant of hair grafts	18
Pan-genomic and comparative analysis of Pediococcus pentosaceus focused on the in silico assessment of pediocin-like bacteriocins	18
Linkage and association analyses reveal that hub genes in energy-flow and lipid biosynthesis pathways form a cluster in upland cotton	18
MOVIS: A multi-omics software solution for multi-modal time-series clustering, embedding, and visualizing tasks	18
Unleashing high content screening in hit detection – Benchmarking AI workflows including novelty detection	18
iResNetDM: An interpretable deep learning approach for four types of DNA methylation modification prediction	18
Osmolyte-induced protein stability changes explained by graph theory	18
Bacterial low-abundant taxa are key determinants of a healthy airway metagenome in the early years of human life	18
Non-coding antisense transcripts: fine regulation of gene expression in cancer	18
A Nano Risk Governance Portal supporting risk governance of nanomaterials and nano-enabled products	18
Transcriptomic signatures associated with autoimmune thyroiditis in papillary thyroid carcinoma and cancer immunotherapy-induced thyroid dysfunction	18
Recognition of immune-related tumor antigens and immune subtypes for mRNA vaccine development in lung adenocarcinoma	18
Computational design of α-amylase from Bacillus licheniformis to increase its activity and stability at high temperatures	18
IBPred: A sequence-based predictor for identifying ion binding protein in phage	18
Family-wide analysis of integrin structures predicted by AlphaFold2	18
AmiCa: Atlas of miRNA-gene correlations in cancer	18
Overcoming the cognition-reality gap in robot-to-human handovers with anisotropic variable force guidance	18
Determining key residues of engineered scFv antibody variants with improved MMP-9 binding using deep sequencing and machine learning	18
BioPrediction-RPI: Democratizing the prediction of interaction between non-coding RNA and protein with end-to-end machine learning	18
Discovery of a new generation of angiotensin receptor blocking drugs: Receptor mechanisms and in silico binding to enzymes relevant to SARS-CoV-2	17
Increased risk of arrhythmias, heart failure, and thrombosis in SARS-CoV-2 positive individuals persists at one year post-infection	17
Corrigendum to “Leveraging large language models to predict antibody biological activity against influenza A hemagglutinin” [Comput Struct Biotechnol J 27 (2025) 1286–1295]	17
HELENA project: Driving innovation in high energy density Li-metal halide solid-state batteries for electric vehicles and aircrafts	17
A potent nonapeptide inhibitor for the CXCL12/HMGB1 heterocomplex: A computational and experimental approach	17
A comprehensive review on computational metabolomics: Advancing multiscale analysis through in-silico approaches	17
The natural product biosynthesis potential of the microbiomes of Earth – Bioprospecting for novel anti-microbial agents in the meta-omics era	17
Starch granules and their size distribution in wheat: Biosynthesis, physicochemical properties and their effect on flour-based food systems	17
Establishment and validation of a cholesterol metabolism-related prognostic signature for hepatocellular carcinoma	17
Evaluation of protein descriptors in computer-aided rational protein engineering tasks and its application in property prediction in SARS-CoV-2 spike glycoprotein	17
iKcr_CNN: A novel computational tool for imbalance classification of human nonhistone crotonylation sites based on convolutional neural networks with focal loss	17
iSanXoT: A standalone application for the integrative analysis of mass spectrometry-based quantitative proteomics data	17
Differential gene expression analysis pipelines and bioinformatic tools for the identification of specific biomarkers: A review	17
Single-cell 5′ RNA sequencing of camelid peripheral B cells provides insights into cellular basis of heavy-chain antibody production	17
Deep learning frameworks for protein–protein interaction prediction	17
Machine learning for metabolic pathway optimization: A review	17
Dynamics of spindle assembly and position checkpoints: Integrating molecular mechanisms with computational models	17
ALDH2 as a potential stem cell-related biomarker in lung adenocarcinoma: Comprehensive multi-omics analysis	17
How to describe the time-dependent dissolution of engineered nanomaterials?	17
Deciphering mitochondrial dysfunction in keratoconus: Insights into ACSL4 from machine learning-based bulk and single-cell transcriptome analyses and experimental validation	17
Integrating whole genome sequencing, methylation, gene expression, topologically associated domain information in regulatory mutation prediction: A study of follicular lymphoma	17
Unlocking the specificity of antimicrobial peptide interactions for membrane-targeted therapies	17
Analysis of the galactomannan binding ability of β-mannosidases, BtMan2A and CmMan5A, regarding their activity and synergism with a β-mannanase	17
The nucleotide landscape of polyXY regions	17
Lateral walking gait phase recognition for hip exoskeleton by denoising autoencoder-LSTM	16
Multidimensional morphological analysis of live sperm based on multiple-target tracking	16
Liquid-liquid phase separation in hair cell stereocilia development and maintenance	16
SortPred: The first machine learning based predictor to identify bacterial sortases and their classes using sequence-derived information	16
An informatic workflow for the enhanced annotation of excretory/secretory proteins of Haemonchus contortus	16
Comprehensive analysis of circulating cell-free RNAs in blood for diagnosing non-small cell lung cancer	16
Accurate protein stability predictions from homology models	16
GENI: A web server to identify gene set enrichments in tumor samples	16
Random survival forest model identifies novel biomarkers of event-free survival in high-risk pediatric acute lymphoblastic leukemia	16