Computational Biology and Chemistry

Article	Citations
Integrated consensus genetic map and genomic scaffold re-ordering of oil palm (Elaeis guineensis) genome	169
The interaction of methotrexate with the human C5a and its potential therapeutic implications	106
Computational investigations of indanedione and indanone derivatives in drug discovery: Indanone derivatives inhibits cereblon, an E3 ubiquitin ligase component	80
Investigation of mesenchymal stem cell secretome on breast cancer gene expression: A bioinformatic approach to identify differentially expressed genes, functional networks, and potential therapeutic t	63
Construction of the small intestine on molecular dynamics simulation and preliminary exploration of drug intestinal absorption prediction	45
Editorial Board	42
Computational insights into irinotecan's interaction with UBE2I in ovarian and endometrial cancers	40
Editorial Board	40
Editorial Board	40
Multi-scale DNA language model improves 6 mA binding sites prediction	39
Implications of trinodal inhibitions and drug repurposing in MAPK pathway: A putative remedy for breast cancer	36
Identification of angiogenesis-related subtypes and risk models for predicting the prognosis of gastric cancer patients	35
Comprehensive analyses of bioinformatics applications in the fight against COVID-19 pandemic	33
A novel parallel feature rank aggregation algorithm for gene selection applied to microarray data classification	32
Computational analysis of the interactions between Ebselen and derivatives with the active site of the main protease from SARS-CoV-2	31
Decision tree classifier based on topological characteristics of subgraph for the mining of protein complexes from large scale PPI networks	30
Classical molecular dynamics simulation identifies catechingallate as a promising antiviral polyphenol against MPOX palmitoylated surface protein	30
New thiazolidine-2,4-diones as effective anti-proliferative and anti-VEGFR-2 agents: Design, synthesis, in vitro, docking, MD simulations, DFT, ADMET, and toxicity studies	29
Editorial Board	28
Identification of oil palm cis-regulatory elements based on DNA free energy and single nucleotide polymorphism density	27
Identification of calcineurin as a predictor of oocyte quality and fertilization competence based on microarray data	27
Molecular insights into the mechanism of sugar-modified enkephalin binding to opioid receptors	27
SSA: Subset sum approach to protein β-sheet structure prediction	27
Computational analyses of the interactome between TNF and TNFR superfamilies	26
Exploring fingerprints for antidiabetic therapeutics related to peroxisome proliferator-activated receptor gamma (PPARγ) modulators: A chemometric modeling approach	25

Netting into the Sophoretin pool: An approach to trace GSTP1 inhibitors for reversing chemoresistance	25
Amyloid β fibrils disruption by kolaviron: Molecular docking and extended molecular dynamics simulation studies	23
Exploration of functional relations among differentially co-expressed genes identifies regulators in glioblastoma	22
Cerebral aneurysm evolution modeling from microstructural computational models to machine learning: A review	21
Bisbenzylisoquinolines from Cissampelos pareira L. as antimalarial agents: Molecular docking, pharmacokinetics analysis, and molecular dynamic simulation studies	21
Integrated structure-guided computational design of novel substituted quinolizin-4-ones as Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors	20
Thiazole inhibitors of α-glucosidase: Positional isomerism modulates selectivity, enzyme binding and potency of inhibition	20
Inflammation inhibitory activity of green tea, soybean, and guava extracts during Sars-Cov-2 infection through TNF protein in cytokine storm	20
A global report on the dynamics of COVID-19 with quarantine and hospitalization: A fractional order model with non-local kernel	19
MSFF-MA-DDI: Multi-Source Feature Fusion with Multiple Attention blocks for predicting Drug–Drug Interaction events	19
Interactions between DNA and the acridine intercalator: A computational study	19
Vector embeddings by sequence similarity and context for improved compression, similarity search, clustering, organization, and manipulation of cDNA libraries	18
SNSynergy: Similarity network-based machine learning framework for synergy prediction towards new cell lines and new anticancer drug combinations	18
CopyMix: Mixture model based single-cell clustering and copy number profiling using variational inference	18
STRIDER: Steric hindrance and metal coordination identifier	18
Impact of calcium ions on the structural and dynamic properties of heparin oligosaccharides by computational analysis	18
Reliable estrogen-related prognostic signature for uterine corpus endometrial carcinoma	17
Comparative in Silico study of apigenin and its dimeric forms on PIM1 kinase in glioblastoma multiform	17
Classification and prediction of variants associated with hearing loss using sequence information in the vicinity of mutation sites	17
An ensemble of bioinformatics and machine learning approaches to identify shared breast cancer biomarkers among diverse populations	17
Machine learning approaches for predicting craniofacial anomalies with graph neural networks	17
An efficient new method of ytterbium(III) triflate catalysis approach to the synthesis of substituted pyrroles: DFT, ADMET, and molecular docking investigations	16
BAT-Net: An enhanced RNA Secondary Structure prediction via bidirectional GRU-based network with attention mechanism	16
Catalytic activity in vitro of the human protein kinase ASK1 mutants: Experimental and molecular simulation study	16
Gene-expression profile analysis to disclose diagnostics and therapeutics biomarkers for thyroid carcinoma	16
P-FARFAR2: A multithreaded greedy approach to sampling low-energy RNA structures in Rosetta FARFAR2	16
Graph-ETMB: A graph neural network-based model for tumour mutation burden estimation	16
An assessment of crucial structural contributors of HDAC6 inhibitors through fragment-based non-linear pattern recognition and molecular dynamics simulation approaches	16
GAP positions catalytic H-Ras residue Q61 for GTP hydrolysis in molecular dynamics simulations, complicating chemical rescue of Ras deactivation	16
Targeting AR-positive breast cancer cells via drug repurposing approach	16
RDDL: A systematic ensemble pipeline tool that streamlines balancing training schemes to reduce the effects of data imbalance in rare-disease-related deep-learning applications	15
Tensor improve equivariant graph neural network for molecular dynamics prediction	15
FusPB-ESM2: Fusion model of ProtBERT and ESM-2 for cell-penetrating peptide prediction	15
SME-MFP: A novel spatiotemporal neural network with multiangle initialization embedding toward multifunctional peptides prediction	15
Modelling the transport mechanism of organic molecules into cell membranes: The role of organic solvents	14
Editorial Board	14
Metaheuristics for multiple sequence alignment: A systematic review	14
Editorial	14
A comprehensive investigation regarding the clinical significance of ITGB4 in oral squamous cell carcinoma combining immunohistochemistry, RNA-seq, and microarray data	13
Transcriptome analysis reveals mechanisms of metabolic detoxification and immune responses following farnesyl acetate treatment in Metisa plana	13
UmamiPreDL: Deep learning model for umami taste prediction of peptides using BERT and CNN	13
NeuralCodOpt: Codon optimization for the development of DNA vaccines	13
A computational study of structural analysis of Class I human glucose-6-phosphate dehydrogenase (G6PD) variants: Elaborating the correlation to chronic non-spherocytic hemolytic anemia (CNSHA)	13
Editorial Board	13
Deep protein representations enable recombinant protein expression prediction	13
Computational analysis of substrate recognition of Sars-Cov-2 Mpro main protease	13
Discovery of small-molecule PD-1/PD-L1 antagonists through combined virtual screening and experimental validation	13
Identification of phytoestrogens as sirtuin inhibitor against breast cancer: Multitargeted approach	13
A computational essential dynamics approach to investigate structural influences of ligand binding on Papain like protease from SARS-CoV-2	12
The marijuana-schizophrenia multifaceted nexus: Connections and conundrums towards neurophysiology	12

Integrated deep learning model for automatic detection and classification of stenosis in coronary angiography	12
Human drug-pathway association prediction based on network consistency projection	12
A composite ranking of risk factors for COVID-19 time-to-event data from a Turkish cohort	12
Fractional whale driving training-based optimization enabled transfer learning for detecting autism spectrum disorder	12
Machine learning and molecular subtyping reveal the impact of diverse patterns of cell death on the prognosis and treatment of hepatocellular carcinoma	11
MMR: A Multi-view Merge Representation model for Chemical-Disease relation extraction	11
ANNInter: A platform to explore ncRNA-ncRNA interactome of Arabidopsis thaliana	11
Computational exploration of Ganoderma lucidum metabolites as potential anti-atherosclerotic agents: Insights from molecular docking and dynamics simulations	11
Synthesis, structural elucidation, DFT calculation, biological studies and DNA interaction of some aryl hydrazone Cr3+, Fe3+, and Cu2+ chelates	11
Editorial Board	11
Osmotic pressure induced by extracellular matrix drives Bacillus subtilis biofilms' self-healing	11
ACDMBI: A deep learning model based on community division and multi-source biological information fusion predicts essential proteins	11
CNVABNN: An AdaBoost algorithm and neural networks-based detection of copy number variations from NGS data	11
Mixed model-based eQTL analysis reveals lncRNAs associated with regulation of genes involved in sex determination and spermatogenesis: The key to understanding human gender imbalance	11
Deep2Pep: A Deep Learning Method in Multi-label Classification of Bioactive Peptide	11
Dual computational and biological assessment of some promising nucleoside analogs against the COVID-19-Omicron variant	10
TopMarker: Computational screening biomarkers of hepatocellular carcinoma from transcriptome and interactome based on differential network topological parameters	10
LPI-CSFFR: Combining serial fusion with feature reuse for predicting LncRNA-protein interactions	10
Acknowledgements to 2019 Reviewers	10
Towards development of new antimalarial compounds through in silico and in vitro assays	10
Phytocompounds of Senecio candicans as potential acetylcholinesterase inhibitors targeting Alzheimer's disease: A structure-based virtual screening and molecular dynamics simulation study	10
Antihyperlipidemic mechanisms of a formula containing Curcuma xanthorrhiza, Sechium edule, and Syzigium polyanthum: In silico and in vitro studies	10
Designing, characterization, biological, DFT, and molecular docking analysis for new FeAZD, NiAZD, and CuAZD complexes incorporating 1-(2-hydroxyphenylazo)− 2-naphthol (H2AZD)	10
Using a dual immunoinformatics and bioinformatics approach to design a novel and effective multi-epitope vaccine against human torovirus disease	10
Integrating multiple sequence features for identifying anticancer peptides	10
Identifying potential Alzheimer's disease therapeutics through GSK-3β inhibition: A molecular docking and dynamics approach	10
Designing, DFT, biological, & molecular docking analysis of new Iron(III) & copper(II) complexes incorporating 1-{[-(2-Hydroxyphenyl)methylene]amino}−5,5-diphenylimidazolidine-2,4-dione (PHNS)	10
Comparative analysis of simple sequence repeats and synteny across ten Oryza species: Implications for stress response and genetic diversity	10
The prevalence of dementia in humans could be the result of a functional adaptation	9
Integrated in silico and experimental discovery of trimeric peptide ligands targeting Butyrylcholinesterase	9
SE-BLTCNN: A channel attention adapted deep learning model based on PSSM for membrane protein classification	9
Phytoflavonoids as alternative therapeutic effect for melanoma: Integrative Network pharmacology, molecular dynamics and drug-likeness profiling for lead discovery	9
A Boolean model of the oncogene role of FAM111B in lung adenocarcinoma	9
Correlation intensity index-index of ideality of correlation: A hyphenated target function for furtherance of MAO-B inhibitory activity assessment	9
In silico profiling, docking analysis, and protein interactions of secondary metabolites in Musa spp. Against the SGE1 protein of Fusarium oxysporum f. sp. cubense	9
Investigating Lycotoxin-An1a (An1a), a defense antiviral peptide from Alopecosa nagpag venom as prospective anti-dengue agent against DENV-2 NS2B-NS3 protease	9
Exploring potential molecular targets and therapeutic efficacy of beauvericin in triple-negative breast cancer cells	9
Intrinsic relative preference profile of pan-kinase inhibitor drug staurosporine towards the clinically occurring gatekeeper mutations in Protein Tyrosine Kinases	9
Integrative bioinformatics analysis of immune activation and gene networks in pediatric septic arthritis	9
Exploring of antioxidant and antibacterial properties of novel 1,3,4-thiadiazole derivatives: Facile synthesis, structural elucidation and DFT approach to antioxidant characteristics	9
A structure-based approach to discover a potential isomerase Pin1 inhibitor for cancer therapy using computational simulation and biological studies	9
Visualization of UV and ECD spectra of E&Z isomers of N-(4′-Hydroxy-cinnamoyl)− 5- hydroxyanthranilic acid	9
Identification and validation of miR-21 key genes in cervical cancer through an integrated bioinformatics approach	9
DeepOCR: A multi-species deep-learning framework for accurate identification of open chromatin regions in livestock	9
16S amplicon sequencing and functional gene prediction of microbial community in Inner West Aegean, Turkey	9
Unveiling novel type 1 inhibitors for targeting LIM kinase 2 (LIMK2) for cancer therapeutics: An integrative pharmacoinformatics approach	9
ACP-ESM2: The prediction of anticancer peptides based on pre-trained classifier	9
Statistical analysis of the unique characteristics of secondary structures in proteins	9
Enhancing gene regulatory networks inference through hub-based data integration	9
Prognostic significance of a 3-gene ferroptosis-related signature in lung cancer via LASSO analysis and cellular functions of UBE2Z	8
Machine learning and molecular simulation ascertain antimicrobial peptide against Klebsiella pneumoniae from public database	8
Exploring enzyme inhibition profiles of novel halogenated chalcone derivatives on some metabolic enzymes: Synthesis, characterization and molecular modeling studies	8
Mining channel-regulated peptides from animal venom by integrating sequence semantics and structural information	8
The method predicting interaction between protein targets and small-molecular ligands with the wide applicability domain	8
Novel 1,4 benzothiazine 3-one derivatives as anticonvulsant agents: Design, synthesis, biological evaluation and computational studies	8
Designing of thiazolidinones against chicken pox, monkey pox, and hepatitis viruses: A computational approach	8
Exploring casual effects and shared molecular mechanism between psoriasis and liver cancer through Mendelian randomization and comprehensive bioinformatic analyses	8
Screening of the effective sites of Cichorium glandulosum against hyperuricemia combined with hyperlipidemia and its network pharmacology analysis	8
Molecular dynamic simulation analysis of SARS-CoV-2 spike mutations and evaluation of ACE2 from pets and wild animals for infection risk	8
Green synthesis of selenium based N-heterocyclic carbene compounds; structural, in-vitro anticancer and molecular docking studies	8
Investigating pH-induced conformational switch in PIM-1: An integrated multi spectroscopic and MD simulation study	8
Robust biomarker screening from gene expression data by stable machine learning-recursive feature elimination methods	8
Co-expression network and survival analysis of breast cancer inflammation and immune system hallmark genes	8
Virtual screening of polyherbal compounds for AKT1 and HSPB1 inhibition in breast cancer apoptosis pathway	8
Editorial Board	8
Pharmacoinformatics-based prediction of Checkpoint kinase-1 inhibitors from Momordica charantia Linn. for cancer	7
Integrated computational approaches for designing potent pyrimidine-based CDK9 inhibitors: 3D-QSAR, docking, and molecular dynamics simulations	7
Cancer detection with various classification models: A comprehensive feature analysis using HMM to extract a nucleotide pattern	7
K1K2NN: A novel multi-label classification approach based on neighbors for predicting COVID-19 drug side effects	7
Identification of potential therapeutic targets for stroke using data mining, network analysis, enrichment, and docking analysis	7
Reconstruction of the binding pathway of an anti-HIV drug, Indinavir, in complex with the HTLV-1 protease using unaggregated unbiased molecular dynamics simulation	7
A deep-SIQRV epidemic model for COVID-19 to access the impact of prevention and control measures	7
Theoretical Investigations of a point mutation affecting H5 Hemagglutinin’s receptor binding preference	7
Design, synthesis, In-vitro, In-silico and DFT studies of novel functionalized isoxazoles as antibacterial and antioxidant agents	7
Harnessing the druggability at orthosteric and allosteric sites of PD-1 for small molecule discovery by an integrated in silico pipeline	7
Real-to-bin conversion for protein residue distances	7
Multiscale modeling of the cellular uptake of C6 peptide-siRNA complexes	7
Multiple omics-based machine learning reveals specific macrophage sub-clusters in renal ischemia-reperfusion injury and constructs predictive models for transplant outcomes	7
Investigation of dual inhibition of antibacterial and antiarthritic drug candidates using combined approach including molecular dynamics, docking and quantum chemical methods	7
AMPCDA: Prediction of circRNA–disease associations by utilizing attention mechanisms on metapaths	7

Halting aberrant DNA methylation via in silico Identification of potent inhibitors of DNMT3B enzyme: Atomistic insights	7
An open source in silico workflow to assist in the design of fusion proteins	7
In silico exploration of CB2 receptor agonist in the management of neuroinflammatory conditions by pharmacophore modeling	7
IoT based healthcare system using fractional dung beetle optimization enabled deep learning for breast cancer classification	7
Cellular and molecular level host-pathogen interactions in Francisella tularensis: A microbial gene network study	7
ARGai 1.0: A GAN augmented in silico approach for identifying resistant genes and strains in E. coli using vision transformer	7
Acknowledgements to 2020 Reviewers	7
GEHGAN: CircRNA–disease association prediction via graph embedding an	6
Transfer learning with molecular graph convolutional networks for accurate modeling and representation of bioactivities of ligands targeting GPCRs without sufficient data	6
Exploring the interaction of phytochemicals from Hibiscus rosa-sinensis flowers with glucosidase and acetylcholinesterase: An integrated in vitro and in silico approach	6
Vaginal birth after cesarean section prediction model for Jordanian population	6
CTDN (Convolutional Temporal Based Deep‐ Neural Network): An Improvised Stacked Hybrid Computational Approach for Anticancer Drug Response Prediction	6
Non-kin selection enhances complexity in cooperation: A unified quantitative law	6
PayloadGenX, a multi-stage hybrid virtual screening approach for payload design: A microtubule inhibitor case study	6
TSSUNet-MB – ab initio identification of σ70 promoter transcription start sites in Escherichia coli using deep multitask learning	6
Non-homogeneous Poisson and renewal processes as spatial models for cancer mutation	6
Glycosylation is key for enhancing drug recognition into spike glycoprotein of SARS-CoV-2	6
Effects of 1,4-dihydropyridine derivatives on cell injury and mTOR of HepG2 and 3D-QSAR study	6
Encoding the space of protein-protein binding interfaces by artificial intelligence	6
Advancing Drug-Target Interaction prediction with BERT and subsequence embedding	6
Uncovering the antidiabetic potential of heart-friendly and diuretic bioactive compounds through computer-based drug design	6
N-glycosylation reinforces interaction of immune checkpoint TIM-3 with a small molecule ligand	6
A small-scale data driven and graph neural network based toxicity prediction method of compounds	6
Where is the mind within the brain? Transient selection of subnetworks by metabotropic receptors and G protein-gated ion channels	6
Cytokine expression patterns: A single-cell RNA sequencing and machine learning based roadmap for cancer classification	6
A novel intelligent framework for assessing within-host transmission dynamics of Chikungunya virus using an unsupervised stochastic neural network approach	6
Ligand binding free energy evaluation by Monte Carlo Recursion	6
Lycopene destabilizes preformed Aβ fibrils: Mechanistic insights from all-atom molecular dynamics simulation	6
A novel prognostic risk score model based on RNA editing level in lower-grade glioma	6
Integrating classic AI and agriculture: A novel model for predicting insecticide-likeness to enhance efficiency in insecticide development	6
Exploring the value of pleural fluid biomarkers for complementary pleural effusion disease examination	6
Planning biosynthetic pathways of target molecules based on metabolic reaction prediction and AND-OR tree search	6
In silico identification of candidate miRNA-encoded Peptides in four Fabaceae species	6