Computational Biology and Chemistry

Article	Citations
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	180
Classical molecular dynamics simulation identifies catechingallate as a promising antiviral polyphenol against MPOX palmitoylated surface protein	110
Computational insights into irinotecan's interaction with UBE2I in ovarian and endometrial cancers	82
The interaction of methotrexate with the human C5a and its potential therapeutic implications	67
Comprehensive analyses of bioinformatics applications in the fight against COVID-19 pandemic	50
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	47
Implications of trinodal inhibitions and drug repurposing in MAPK pathway: A putative remedy for breast cancer	46
Identification and validation of biomarkers in Alzheimer's disease based on machine learning algorithms and single-cell sequencing analysis	42
Amino acid sequence-based IDR classification using ensemble machine learning and quantum neural networks	41
Multi-scale DNA language model improves 6 mA binding sites prediction	41
Identification of angiogenesis-related subtypes and risk models for predicting the prognosis of gastric cancer patients	37
A novel parallel feature rank aggregation algorithm for gene selection applied to microarray data classification	36
Decision tree classifier based on topological characteristics of subgraph for the mining of protein complexes from large scale PPI networks	35
Editorial Board	34
Computational analysis of the interactions between Ebselen and derivatives with the active site of the main protease from SARS-CoV-2	34
Editorial Board	32
Construction of the small intestine on molecular dynamics simulation and preliminary exploration of drug intestinal absorption prediction	32
Integrated consensus genetic map and genomic scaffold re-ordering of oil palm (Elaeis guineensis) genome	30
Computational investigations of indanedione and indanone derivatives in drug discovery: Indanone derivatives inhibits cereblon, an E3 ubiquitin ligase component	30
Editorial Board	30
Editorial Board	29
Exploring fingerprints for antidiabetic therapeutics related to peroxisome proliferator-activated receptor gamma (PPARγ) modulators: A chemometric modeling approach	29
Using the Reactome Graph Database to generate pathway fingerprints for cancer-related genes, and using the fingerprints to gain insights into cancer, comorbidity, and cancer gene networks	28
Understanding the IDH1 missense SNPs on expression of genes involved in Glioblastoma multiforme	27
Thiazole inhibitors of α-glucosidase: Positional isomerism modulates selectivity, enzyme binding and potency of inhibition	27

Integrated structure-guided computational design of novel substituted quinolizin-4-ones as Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors	27
Interactions between DNA and the acridine intercalator: A computational study	25
A global report on the dynamics of COVID-19 with quarantine and hospitalization: A fractional order model with non-local kernel	24
Netting into the Sophoretin pool: An approach to trace GSTP1 inhibitors for reversing chemoresistance	24
Identification of oil palm cis-regulatory elements based on DNA free energy and single nucleotide polymorphism density	22
MSFF-MA-DDI: Multi-Source Feature Fusion with Multiple Attention blocks for predicting Drug–Drug Interaction events	22
Computational analyses of the interactome between TNF and TNFR superfamilies	22
Inflammation inhibitory activity of green tea, soybean, and guava extracts during Sars-Cov-2 infection through TNF protein in cytokine storm	21
Cerebral aneurysm evolution modeling from microstructural computational models to machine learning: A review	21
Exploration of functional relations among differentially co-expressed genes identifies regulators in glioblastoma	20
STRIDER: Steric hindrance and metal coordination identifier	20
Bisbenzylisoquinolines from Cissampelos pareira L. as antimalarial agents: Molecular docking, pharmacokinetics analysis, and molecular dynamic simulation studies	20
Molecular insights into the mechanism of sugar-modified enkephalin binding to opioid receptors	20
SNSynergy: Similarity network-based machine learning framework for synergy prediction towards new cell lines and new anticancer drug combinations	20
CopyMix: Mixture model based single-cell clustering and copy number profiling using variational inference	19
Impact of calcium ions on the structural and dynamic properties of heparin oligosaccharides by computational analysis	19
Tensor improve equivariant graph neural network for molecular dynamics prediction	19
Comparative in Silico study of apigenin and its dimeric forms on PIM1 kinase in glioblastoma multiform	18
Classification and prediction of variants associated with hearing loss using sequence information in the vicinity of mutation sites	18
Reliable estrogen-related prognostic signature for uterine corpus endometrial carcinoma	18
Gene-expression profile analysis to disclose diagnostics and therapeutics biomarkers for thyroid carcinoma	18
Machine learning approaches for predicting craniofacial anomalies with graph neural networks	18
Vector embeddings by sequence similarity and context for improved compression, similarity search, clustering, organization, and manipulation of cDNA libraries	18
BAT-Net: An enhanced RNA Secondary Structure prediction via bidirectional GRU-based network with attention mechanism	17
An ensemble of bioinformatics and machine learning approaches to identify shared breast cancer biomarkers among diverse populations	17
GAP positions catalytic H-Ras residue Q61 for GTP hydrolysis in molecular dynamics simulations, complicating chemical rescue of Ras deactivation	17
FusPB-ESM2: Fusion model of ProtBERT and ESM-2 for cell-penetrating peptide prediction	17
P-FARFAR2: A multithreaded greedy approach to sampling low-energy RNA structures in Rosetta FARFAR2	17
SME-MFP: A novel spatiotemporal neural network with multiangle initialization embedding toward multifunctional peptides prediction	17
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	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
Catalytic activity in vitro of the human protein kinase ASK1 mutants: Experimental and molecular simulation study	16
Targeting AR-positive breast cancer cells via drug repurposing approach	16
Fractional whale driving training-based optimization enabled transfer learning for detecting autism spectrum disorder	15
Conformational Dynamics and Energetic Perturbations in Human β-Spectrin-II Mediated by Calpain Cleavage-Related Mutations: Insights from Enhanced Sampling Simulations	15
An efficient new method of ytterbium(III) triflate catalysis approach to the synthesis of substituted pyrroles: DFT, ADMET, and molecular docking investigations	15
Transcriptome analysis reveals mechanisms of metabolic detoxification and immune responses following farnesyl acetate treatment in Metisa plana	15
Deep2Pep: A deep learning method in multi-label classification of bioactive peptide	14
im7G-DCT: A two-branch strategy model based on improved DenseNet and transformer for m7G site prediction	14
The marijuana-schizophrenia multifaceted nexus: Connections and conundrums towards neurophysiology	14
NeuralCodOpt: Codon optimization for the development of DNA vaccines	14
Identification of phytoestrogens as sirtuin inhibitor against breast cancer: Multitargeted approach	14
UmamiPreDL: Deep learning model for umami taste prediction of peptides using BERT and CNN	14
scDGG: Dynamic gene graphs for enhancing clustering analysis of single-cell RNA sequencing data via spatiotemporal representations	14
Integrated deep learning model for automatic detection and classification of stenosis in coronary angiography	13
Deep protein representations enable recombinant protein expression prediction	13
A comprehensive investigation regarding the clinical significance of ITGB4 in oral squamous cell carcinoma combining immunohistochemistry, RNA-seq, and microarray data	13
A computational essential dynamics approach to investigate structural influences of ligand binding on Papain like protease from SARS-CoV-2	13
A composite ranking of risk factors for COVID-19 time-to-event data from a Turkish cohort	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
Human drug-pathway association prediction based on network consistency projection	13
Modelling the transport mechanism of organic molecules into cell membranes: The role of organic solvents	13
Discovery of small-molecule PD-1/PD-L1 antagonists through combined virtual screening and experimental validation	12
Computational exploration of Ganoderma lucidum metabolites as potential anti-atherosclerotic agents: Insights from molecular docking and dynamics simulations	12
Editorial Board	12
Editorial Board	12
Editorial	12
Synthesis, structural elucidation, DFT calculation, biological studies and DNA interaction of some aryl hydrazone Cr3+, Fe3+, and Cu2+ chelates	12
Computational analysis of substrate recognition of Sars-Cov-2 Mpro main protease	12
Editorial Board	12
Machine learning and molecular subtyping reveal the impact of diverse patterns of cell death on the prognosis and treatment of hepatocellular carcinoma	12
Integrating multiple sequence features for identifying anticancer peptides	11
ACDMBI: A deep learning model based on community division and multi-source biological information fusion predicts essential proteins	11
Designing, characterization, biological, DFT, and molecular docking analysis for new FeAZD, NiAZD, and CuAZD complexes incorporating 1-(2-hydroxyphenylazo)− 2-naphthol (H2AZD)	11
TopMarker: Computational screening biomarkers of hepatocellular carcinoma from transcriptome and interactome based on differential network topological parameters	11
Antihyperlipidemic mechanisms of a formula containing Curcuma xanthorrhiza, Sechium edule, and Syzigium polyanthum: In silico and in vitro studies	11
MMR: A Multi-view Merge Representation model for Chemical-Disease relation extraction	11
Towards development of new antimalarial compounds through in silico and in vitro assays	11
Using a dual immunoinformatics and bioinformatics approach to design a novel and effective multi-epitope vaccine against human torovirus disease	11
Dual computational and biological assessment of some promising nucleoside analogs against the COVID-19-Omicron variant	11
ANNInter: A platform to explore ncRNA-ncRNA interactome of Arabidopsis thaliana	11
Comparative anti-oxidant and anti-inflammatory study of diverse honey types of Kashmir valley through In Vitro, analytical chemistry and computational approach	11
Phytocompounds of Senecio candicans as potential acetylcholinesterase inhibitors targeting Alzheimer's disease: A structure-based virtual screening and molecular dynamics simulation study	11
LPI-CSFFR: Combining serial fusion with feature reuse for predicting LncRNA-protein interactions	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	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
In silico profiling, docking analysis, and protein interactions of secondary metabolites in Musa spp. Against the SGE1 protein of Fusarium oxysporum f. sp. cubense	10
A Boolean model of the oncogene role of FAM111B in lung adenocarcinoma	10
Osmotic pressure induced by extracellular matrix drives Bacillus subtilis biofilms' self-healing	10
Statistical analysis of the unique characteristics of secondary structures in proteins	10
Comparative analysis of simple sequence repeats and synteny across ten Oryza species: Implications for stress response and genetic diversity	10
CNVABNN: An AdaBoost algorithm and neural networks-based detection of copy number variations from NGS data	10
Identifying potential Alzheimer's disease therapeutics through GSK-3β inhibition: A molecular docking and dynamics approach	10
A structure-based approach to discover a potential isomerase Pin1 inhibitor for cancer therapy using computational simulation and biological studies	10
ACP-ESM2: The prediction of anticancer peptides based on pre-trained classifier	10
Investigating pH-induced conformational switch in PIM-1: An integrated multi spectroscopic and MD simulation study	9
Visualization of UV and ECD spectra of E&Z isomers of N-(4′-Hydroxy-cinnamoyl)− 5- hydroxyanthranilic acid	9
Enhancing gene regulatory networks inference through hub-based data integration	9
Editorial Board	9
Transcriptomic analysis of human castration-resistant prostate cancer: Insights into novel therapeutic strategies	9
Phytoflavonoids as alternative therapeutic effect for melanoma: Integrative Network pharmacology, molecular dynamics and drug-likeness profiling for lead discovery	9
Exploring potential molecular targets and therapeutic efficacy of beauvericin in triple-negative breast cancer cells	9
Correlation intensity index-index of ideality of correlation: A hyphenated target function for furtherance of MAO-B inhibitory activity assessment	9
16S amplicon sequencing and functional gene prediction of microbial community in Inner West Aegean, Turkey	9
Prognostic significance of a 3-gene ferroptosis-related signature in lung cancer via LASSO analysis and cellular functions of UBE2Z	9
Integrative bioinformatics analysis of immune activation and gene networks in pediatric septic arthritis	9
Acknowledgements to 2019 Reviewers	9
Identification and validation of miR-21 key genes in cervical cancer through an integrated bioinformatics approach	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
DeepOCR: A multi-species deep-learning framework for accurate identification of open chromatin regions in livestock	9
Machine learning and molecular simulation ascertain antimicrobial peptide against Klebsiella pneumoniae from public database	8
Integrated in silico and experimental discovery of trimeric peptide ligands targeting Butyrylcholinesterase	8
Exploring enzyme inhibition profiles of novel halogenated chalcone derivatives on some metabolic enzymes: Synthesis, characterization and molecular modeling studies	8
Exploring casual effects and shared molecular mechanism between psoriasis and liver cancer through Mendelian randomization and comprehensive bioinformatic analyses	8
In silico exploration of CB2 receptor agonist in the management of neuroinflammatory conditions by pharmacophore modeling	8
A novel Convolutional Shuffle Attention Xtreme Gradient Boost Network for improved lung cancer detection using computed tomography images	8
The prevalence of dementia in humans could be the result of a functional adaptation	8
Designing of thiazolidinones against chicken pox, monkey pox, and hepatitis viruses: A computational approach	8
Investigating Lycotoxin-An1a (An1a), a defense antiviral peptide from Alopecosa nagpag venom as prospective anti-dengue agent against DENV-2 NS2B-NS3 protease	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
Pharmacoinformatics-based prediction of Checkpoint kinase-1 inhibitors from Momordica charantia Linn. for cancer	8
Robust biomarker screening from gene expression data by stable machine learning-recursive feature elimination methods	8
SE-BLTCNN: A channel attention adapted deep learning model based on PSSM for membrane protein classification	8
Novel 1,4 benzothiazine 3-one derivatives as anticonvulsant agents: Design, synthesis, biological evaluation and computational studies	8
Unveiling novel type 1 inhibitors for targeting LIM kinase 2 (LIMK2) for cancer therapeutics: An integrative pharmacoinformatics approach	8
Screening of the effective sites of Cichorium glandulosum against hyperuricemia combined with hyperlipidemia and its network pharmacology analysis	8
An open source in silico workflow to assist in the design of fusion proteins	8
PayloadGenX, a multi-stage hybrid virtual screening approach for payload design: A microtubule inhibitor case study	7
Editorial Board	7
Investigation of dual inhibition of antibacterial and antiarthritic drug candidates using combined approach including molecular dynamics, docking and quantum chemical methods	7
Multiple omics-based machine learning reveals specific macrophage sub-clusters in renal ischemia-reperfusion injury and constructs predictive models for transplant outcomes	7
Harnessing the druggability at orthosteric and allosteric sites of PD-1 for small molecule discovery by an integrated in silico pipeline	7
Integrated computational approaches for designing potent pyrimidine-based CDK9 inhibitors: 3D-QSAR, docking, and molecular dynamics simulations	7
A deep-SIQRV epidemic model for COVID-19 to access the impact of prevention and control measures	7
A novel intelligent framework for assessing within-host transmission dynamics of Chikungunya virus using an unsupervised stochastic neural network approach	7
Integrating classic AI and agriculture: A novel model for predicting insecticide-likeness to enhance efficiency in insecticide development	7
Design, synthesis, In-vitro, In-silico and DFT studies of novel functionalized isoxazoles as antibacterial and antioxidant agents	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

Coevolutionary dynamics of 53BP1 and its impact on TP53 interaction for DNA damage repair	7
Identification of potential therapeutic targets for stroke using data mining, network analysis, enrichment, and docking analysis	7
DICCA-DTA: Diffusion and Contextualized Capsule Attention guided Factorized Cross-Pooling for Drug-Target Affinity prediction	7
Molecular dynamic simulation analysis of SARS-CoV-2 spike mutations and evaluation of ACE2 from pets and wild animals for infection risk	7
ARGai 1.0: A GAN augmented in silico approach for identifying resistant genes and strains in E. coli using vision transformer	7
A small-scale data driven and graph neural network based toxicity prediction method of compounds	7
Cellular and molecular level host-pathogen interactions in Francisella tularensis: A microbial gene network study	7
The method predicting interaction between protein targets and small-molecular ligands with the wide applicability domain	7
Mining channel-regulated peptides from animal venom by integrating sequence semantics and structural information	7
Multiscale modeling of the cellular uptake of C6 peptide-siRNA complexes	7
K1K2NN: A novel multi-label classification approach based on neighbors for predicting COVID-19 drug side effects	7
Prediction of key pathways in hepatocellular carcinoma (HCC): A machine learning approach using a sample pathway information matrix	7
Cancer detection with various classification models: A comprehensive feature analysis using HMM to extract a nucleotide pattern	7
Real-to-bin conversion for protein residue distances	7
Uncovering the antidiabetic potential of heart-friendly and diuretic bioactive compounds through computer-based drug design	7
GEHGAN: CircRNA–disease association prediction via graph embedding an	7
IoT based healthcare system using fractional dung beetle optimization enabled deep learning for breast cancer classification	7
Non-homogeneous Poisson and renewal processes as spatial models for cancer mutation	6
Where is the mind within the brain? Transient selection of subnetworks by metabotropic receptors and G protein-gated ion channels	6
Comments on 'Flexibility of enzymatic transitions as a hallmark of optimized enzyme steady-state kinetics and thermodynamics'	6
A novel prognostic risk score model based on RNA editing level in lower-grade glioma	6
Theoretical Investigations of a point mutation affecting H5 Hemagglutinin’s receptor binding preference	6
AMPCDA: Prediction of circRNA–disease associations by utilizing attention mechanisms on metapaths	6
Computational study and design of effective siRNAs to silence structural proteins associated genes of Indian SARS-CoV-2 strains	6
Exploring the interaction of phytochemicals from Hibiscus rosa-sinensis flowers with glucosidase and acetylcholinesterase: An integrated in vitro and in silico approach	6
Profiling the structural determinants of pyrrolidine derivative as gelatinases (MMP-2 and MMP-9) inhibitors using in silico approaches	6
Differentiating stable and unstable protein using convolution neural network and molecular dynamics simulations	6
OTUCD: Unsupervised GCN based metagenomics non-overlapping community detection	6
TSSUNet-MB – ab initio identification of σ70 promoter transcription start sites in Escherichia coli using deep multitask learning	6
Vaginal birth after cesarean section prediction model for Jordanian population	6
Cytokine expression patterns: A single-cell RNA sequencing and machine learning based roadmap for cancer classification	6
Ligand binding free energy evaluation by Monte Carlo Recursion	6
Design and characterization of defined alpha-helix mini-proteins with intrinsic cell permeability	6
An efficient Burrows–Wheeler transform-based aligner for short read mapping	6
Lycopene destabilizes preformed Aβ fibrils: Mechanistic insights from all-atom molecular dynamics simulation	6
Encoding the space of protein-protein binding interfaces by artificial intelligence	6
Acknowledgements to 2020 Reviewers	6
Non-kin selection enhances complexity in cooperation: A unified quantitative law	6
Targeting cyclin-dependent kinase 2 CDK2: Insights from molecular docking and dynamics simulation – A systematic computational approach to discover novel cancer therapeutics	6
Accelerating drug discovery targeting dihydroorotate dehydrogenase using machine learning and generative AI approaches	6
ETENLNC: An end to end lncRNA identification and analysis framework to facilitate construction of known and novel lncRNA regulatory networks	6
In silico identification of candidate miRNA-encoded Peptides in four Fabaceae species	6
Terpenoid phytocompounds from mangrove plant Xylocarpus moluccensis as possible inhibitors against SARS-CoV-2: In silico strategy	6
CTDN (Convolutional Temporal Based Deep‐ Neural Network): An Improvised Stacked Hybrid Computational Approach for Anticancer Drug Response Prediction	6
Advancing Drug-Target Interaction prediction with BERT and subsequence embedding	6
Glycosylation is key for enhancing drug recognition into spike glycoprotein of SARS-CoV-2	6
Halting aberrant DNA methylation via in silico Identification of potent inhibitors of DNMT3B enzyme: Atomistic insights	6
Planning biosynthetic pathways of target molecules based on metabolic reaction prediction and AND-OR tree search	6
Effects of 1,4-dihydropyridine derivatives on cell injury and mTOR of HepG2 and 3D-QSAR study	6
DeepRHD: An efficient hybrid feature extraction technique for protein remote homology detection using deep learning strategies	6
Transfer learning with molecular graph convolutional networks for accurate modeling and representation of bioactivities of ligands targeting GPCRs without sufficient data	6
N-glycosylation reinforces interaction of immune checkpoint TIM-3 with a small molecule ligand	6