Computational Biology and Chemistry

Article	Citations
Integrated consensus genetic map and genomic scaffold re-ordering of oil palm (Elaeis guineensis) genome	152
The interaction of methotrexate with the human C5a and its potential therapeutic implications	105
Computational investigations of indanedione and indanone derivatives in drug discovery: Indanone derivatives inhibits cereblon, an E3 ubiquitin ligase component	77
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	56
Construction of the small intestine on molecular dynamics simulation and preliminary exploration of drug intestinal absorption prediction	44
Classical molecular dynamics simulation identifies catechingallate as a promising antiviral polyphenol against MPOX palmitoylated surface protein	40
Editorial Board	36
Editorial Board	36
Computational insights into irinotecan's interaction with UBE2I in ovarian and endometrial cancers	35
Editorial Board	35
Implications of trinodal inhibitions and drug repurposing in MAPK pathway: A putative remedy for breast cancer	34
Identification of angiogenesis-related subtypes and risk models for predicting the prognosis of gastric cancer patients	33
Computational analysis of the interactions between Ebselen and derivatives with the active site of the main protease from SARS-CoV-2	30
Comprehensive analyses of bioinformatics applications in the fight against COVID-19 pandemic	30
Multi-scale DNA language model improves 6 mA binding sites prediction	29
Decision tree classifier based on topological characteristics of subgraph for the mining of protein complexes from large scale PPI networks	28
A novel parallel feature rank aggregation algorithm for gene selection applied to microarray data classification	28
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	27
Identification of oil palm cis-regulatory elements based on DNA free energy and single nucleotide polymorphism density	26
Editorial Board	26
SSA: Subset sum approach to protein β-sheet structure prediction	26
Molecular insights into the mechanism of sugar-modified enkephalin binding to opioid receptors	26
Identification of calcineurin as a predictor of oocyte quality and fertilization competence based on microarray data	25
Netting into the Sophoretin pool: An approach to trace GSTP1 inhibitors for reversing chemoresistance	24
Computational analyses of the interactome between TNF and TNFR superfamilies	24

Bisbenzylisoquinolines from Cissampelos pareira L. as antimalarial agents: Molecular docking, pharmacokinetics analysis, and molecular dynamic simulation studies	24
Cerebral aneurysm evolution modeling from microstructural computational models to machine learning: A review	24
Exploration of functional relations among differentially co-expressed genes identifies regulators in glioblastoma	23
Inflammation inhibitory activity of green tea, soybean, and guava extracts during Sars-Cov-2 infection through TNF protein in cytokine storm	23
Thiazole inhibitors of α-glucosidase: Positional isomerism modulates selectivity, enzyme binding and potency of inhibition	22
Impact of calcium ions on the structural and dynamic properties of heparin oligosaccharides by computational analysis	20
SNSynergy: Similarity network-based machine learning framework for synergy prediction towards new cell lines and new anticancer drug combinations	19
Integrated structure-guided computational design of novel substituted quinolizin-4-ones as Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors	19
Exploring fingerprints for antidiabetic therapeutics related to peroxisome proliferator-activated receptor gamma (PPARγ) modulators: A chemometric modeling approach	19
A global report on the dynamics of COVID-19 with quarantine and hospitalization: A fractional order model with non-local kernel	18
Amyloid β fibrils disruption by kolaviron: Molecular docking and extended molecular dynamics simulation studies	18
MSFF-MA-DDI: Multi-Source Feature Fusion with Multiple Attention blocks for predicting Drug–Drug Interaction events	18
Interactions between DNA and the acridine intercalator: A computational study	18
STRIDER: Steric hindrance and metal coordination identifier	17
An efficient new method of ytterbium(III) triflate catalysis approach to the synthesis of substituted pyrroles: DFT, ADMET, and molecular docking investigations	17
Vector embeddings by sequence similarity and context for improved compression, similarity search, clustering, organization, and manipulation of cDNA libraries	17
CopyMix: Mixture model based single-cell clustering and copy number profiling using variational inference	17
Machine learning approaches for predicting craniofacial anomalies with graph neural networks	16
Comparative in Silico study of apigenin and its dimeric forms on PIM1 kinase in glioblastoma multiform	16
An ensemble of bioinformatics and machine learning approaches to identify shared breast cancer biomarkers among diverse populations	16
Classification and prediction of variants associated with hearing loss using sequence information in the vicinity of mutation sites	16
Reliable estrogen-related prognostic signature for uterine corpus endometrial carcinoma	16
Catalytic activity in vitro of the human protein kinase ASK1 mutants: Experimental and molecular simulation study	15
GAP positions catalytic H-Ras residue Q61 for GTP hydrolysis in molecular dynamics simulations, complicating chemical rescue of Ras deactivation	15
Tensor improve equivariant graph neural network for molecular dynamics prediction	15
SME-MFP: A novel spatiotemporal neural network with multiangle initialization embedding toward multifunctional peptides prediction	15
Targeting AR-positive breast cancer cells via drug repurposing approach	15
MD-UNET: Multi-input dilated U-shape neural network for segmentation of bladder cancer	15
Graph-ETMB: A graph neural network-based model for tumour mutation burden estimation	15
P-FARFAR2: A multithreaded greedy approach to sampling low-energy RNA structures in Rosetta FARFAR2	15
FusPB-ESM2: Fusion model of ProtBERT and ESM-2 for cell-penetrating peptide prediction	14
Gene-expression profile analysis to disclose diagnostics and therapeutics biomarkers for thyroid carcinoma	14
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	14
BAT-Net: An enhanced RNA Secondary Structure prediction via bidirectional GRU-based network with attention mechanism	14
An assessment of crucial structural contributors of HDAC6 inhibitors through fragment-based non-linear pattern recognition and molecular dynamics simulation approaches	14
Metaheuristics for multiple sequence alignment: A systematic review	14
Editorial Board	13
Editorial	13
A comprehensive investigation regarding the clinical significance of ITGB4 in oral squamous cell carcinoma combining immunohistochemistry, RNA-seq, and microarray data	13
Modelling the transport mechanism of organic molecules into cell membranes: The role of organic solvents	13
Transcriptome analysis reveals mechanisms of metabolic detoxification and immune responses following farnesyl acetate treatment in Metisa plana	12
Computational analysis of substrate recognition of Sars-Cov-2 Mpro main protease	12
Editorial Board	12
An assembling strategy for DNA cages with minimum strands	12
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)	12
Discovery of small-molecule PD-1/PD-L1 antagonists through combined virtual screening and experimental validation	12
Fractional whale driving training-based optimization enabled transfer learning for detecting autism spectrum disorder	11
NeuralCodOpt: Codon optimization for the development of DNA vaccines	11
Synthesis, structural elucidation, DFT calculation, biological studies and DNA interaction of some aryl hydrazone Cr3+, Fe3+, and Cu2+ chelates	11
Human drug-pathway association prediction based on network consistency projection	11

The marijuana-schizophrenia multifaceted nexus: Connections and conundrums towards neurophysiology	11
Integrated deep learning model for automatic detection and classification of stenosis in coronary angiography	11
Deep2Pep: A Deep Learning Method in Multi-label Classification of Bioactive Peptide	11
Identification of phytoestrogens as sirtuin inhibitor against breast cancer: Multitargeted approach	11
Deep protein representations enable recombinant protein expression prediction	11
Computational exploration of Ganoderma lucidum metabolites as potential anti-atherosclerotic agents: Insights from molecular docking and dynamics simulations	11
Machine learning and molecular subtyping reveal the impact of diverse patterns of cell death on the prognosis and treatment of hepatocellular carcinoma	11
A composite ranking of risk factors for COVID-19 time-to-event data from a Turkish cohort	11
UmamiPreDL: Deep learning model for umami taste prediction of peptides using BERT and CNN	11
A computational essential dynamics approach to investigate structural influences of ligand binding on Papain like protease from SARS-CoV-2	11
ACDMBI: A deep learning model based on community division and multi-source biological information fusion predicts essential proteins	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
Towards development of new antimalarial compounds through in silico and in vitro assays	10
MMR: A Multi-view Merge Representation model for Chemical-Disease relation extraction	10
Editorial Board	10
CNVABNN: An AdaBoost algorithm and neural networks-based detection of copy number variations from NGS data	10
Antihyperlipidemic mechanisms of a formula containing Curcuma xanthorrhiza, Sechium edule, and Syzigium polyanthum: In silico and in vitro studies	10
A computational analysis of molecular evolution for virulence genes of zoonotic novel coronavirus (COVID-19)	10
ANNInter: A platform to explore ncRNA-ncRNA interactome of Arabidopsis thaliana	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
Statistical analysis of the unique characteristics of secondary structures in proteins	9
Unravelling Pasteurella multocida Toxin (PMT): Structural Insights, Antibiotic Assessment, and Identification of Potential Inhibitors	9
Using a dual immunoinformatics and bioinformatics approach to design a novel and effective multi-epitope vaccine against human torovirus disease	9
Comparative analysis of simple sequence repeats and synteny across ten Oryza species: Implications for stress response and genetic diversity	9
ActTRANS: Functional classification in active transport proteins based on transfer learning and contextual representations	9
Visualization of UV and ECD spectra of E&Z isomers of N-(4′-Hydroxy-cinnamoyl)− 5- hydroxyanthranilic acid	9
Dual computational and biological assessment of some promising nucleoside analogs against the COVID-19-Omicron variant	9
Osmotic pressure induced by extracellular matrix drives Bacillus subtilis biofilms' self-healing	9
TopMarker: Computational screening biomarkers of hepatocellular carcinoma from transcriptome and interactome based on differential network topological parameters	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
A structure-based approach to discover a potential isomerase Pin1 inhibitor for cancer therapy using computational simulation and biological studies	9
LPI-CSFFR: Combining serial fusion with feature reuse for predicting LncRNA-protein interactions	9
Designing, characterization, biological, DFT, and molecular docking analysis for new FeAZD, NiAZD, and CuAZD complexes incorporating 1-(2-hydroxyphenylazo)− 2-naphthol (H2AZD)	9
Integrating multiple sequence features for identifying anticancer peptides	9
Acknowledgements to 2019 Reviewers	9
Identification and validation of miR-21 key genes in cervical cancer through an integrated bioinformatics approach	9
Integrative bioinformatics analysis of immune activation and gene networks in pediatric septic arthritis	8
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
Transcription factors and chaperone proteins play a role in launching a faster response to heat stress and aggregation	8
16S amplicon sequencing and functional gene prediction of microbial community in Inner West Aegean, Turkey	8
Unveiling novel type 1 inhibitors for targeting LIM kinase 2 (LIMK2) for cancer therapeutics: An integrative pharmacoinformatics approach	8
Exploring potential molecular targets and therapeutic efficacy of beauvericin in triple-negative breast cancer cells	8
Exploring of antioxidant and antibacterial properties of novel 1,3,4-thiadiazole derivatives: Facile synthesis, structural elucidation and DFT approach to antioxidant characteristics	8
Enhancing gene regulatory networks inference through hub-based data integration	8
SE-BLTCNN: A channel attention adapted deep learning model based on PSSM for membrane protein classification	8
DeepOCR: A multi-species deep-learning framework for accurate identification of open chromatin regions in livestock	8
Prognostic significance of a 3-gene ferroptosis-related signature in lung cancer via LASSO analysis and cellular functions of UBE2Z	8
Novel 1,4 benzothiazine 3-one derivatives as anticonvulsant agents: Design, synthesis, biological evaluation and computational studies	8
High-throughput virtual screening and microsecond MD simulations to identify potential sugar mimic of the solute-binding protein BlAXBP of the ABC transporter from Bifidobacterium animalis subsp. Lact	8
The prevalence of dementia in humans could be the result of a functional adaptation	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
ACP-ESM2: The prediction of anticancer peptides based on pre-trained classifier	8
A Boolean model of the oncogene role of FAM111B in lung adenocarcinoma	8
Investigating pH-induced conformational switch in PIM-1: An integrated multi spectroscopic and MD simulation study	8
Designing of thiazolidinones against chicken pox, monkey pox, and hepatitis viruses: A computational approach	8
Robust biomarker screening from gene expression data by stable machine learning-recursive feature elimination methods	8
Intrinsic relative preference profile of pan-kinase inhibitor drug staurosporine towards the clinically occurring gatekeeper mutations in Protein Tyrosine Kinases	8
Green synthesis of selenium based N-heterocyclic carbene compounds; structural, in-vitro anticancer and molecular docking studies	8
Correlation intensity index-index of ideality of correlation: A hyphenated target function for furtherance of MAO-B inhibitory activity assessment	8
Exploring casual effects and shared molecular mechanism between psoriasis and liver cancer through Mendelian randomization and comprehensive bioinformatic analyses	7
Co-expression network and survival analysis of breast cancer inflammation and immune system hallmark genes	7
Screening of the effective sites of Cichorium glandulosum against hyperuricemia combined with hyperlipidemia and its network pharmacology analysis	7
Real-to-bin conversion for protein residue distances	7
IoT based healthcare system using fractional dung beetle optimization enabled deep learning for breast cancer classification	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
Editorial Board	7
Mining channel-regulated peptides from animal venom by integrating sequence semantics and structural information	7
Virtual screening of polyherbal compounds for AKT1 and HSPB1 inhibition in breast cancer apoptosis pathway	7
In silico exploration of CB2 receptor agonist in the management of neuroinflammatory conditions by pharmacophore modeling	7
Cellular and molecular level host-pathogen interactions in Francisella tularensis: A microbial gene network study	7
Ensembling machine learning models to boost molecular affinity prediction	7
The method predicting interaction between protein targets and small-molecular ligands with the wide applicability domain	7
Cancer detection with various classification models: A comprehensive feature analysis using HMM to extract a nucleotide pattern	7
An open source in silico workflow to assist in the design of fusion proteins	7
Molecular dynamic simulation analysis of SARS-CoV-2 spike mutations and evaluation of ACE2 from pets and wild animals for infection risk	7
Multiscale modeling of the cellular uptake of C6 peptide-siRNA complexes	7
Integrated computational approaches for designing potent pyrimidine-based CDK9 inhibitors: 3D-QSAR, docking, and molecular dynamics simulations	7

K1K2NN: A novel multi-label classification approach based on neighbors for predicting COVID-19 drug side effects	7
Theoretical Investigations of a point mutation affecting H5 Hemagglutinin’s receptor binding preference	6
Non-homogeneous Poisson and renewal processes as spatial models for cancer mutation	6
AMPCDA: Prediction of circRNA–disease associations by utilizing attention mechanisms on metapaths	6
Lycopene destabilizes preformed Aβ fibrils: Mechanistic insights from all-atom molecular dynamics simulation	6
Halting aberrant DNA methylation via in silico Identification of potent inhibitors of DNMT3B enzyme: Atomistic insights	6
Pharmacoinformatics-based prediction of Checkpoint kinase-1 inhibitors from Momordica charantia Linn. for cancer	6
Design, synthesis, In-vitro, In-silico and DFT studies of novel functionalized isoxazoles as antibacterial and antioxidant agents	6
Encoding the space of protein-protein binding interfaces by artificial intelligence	6
TSSUNet-MB – ab initio identification of σ70 promoter transcription start sites in Escherichia coli using deep multitask learning	6
Comments on 'Flexibility of enzymatic transitions as a hallmark of optimized enzyme steady-state kinetics and thermodynamics'	6
Glycosylation is key for enhancing drug recognition into spike glycoprotein of SARS-CoV-2	6
Integrating classic AI and agriculture: A novel model for predicting insecticide-likeness to enhance efficiency in insecticide development	6
ARGai 1.0: A GAN augmented in silico approach for identifying resistant genes and strains in E. coli using vision transformer	6
Effects of 1,4-dihydropyridine derivatives on cell injury and mTOR of HepG2 and 3D-QSAR study	6
A deep-SIQRV epidemic model for COVID-19 to access the impact of prevention and control measures	6
Investigation of dual inhibition of antibacterial and antiarthritic drug candidates using combined approach including molecular dynamics, docking and quantum chemical methods	6
Uncovering the antidiabetic potential of heart-friendly and diuretic bioactive compounds through computer-based drug design	6
In silico identification of candidate miRNA-encoded Peptides in four Fabaceae species	6
Where is the mind within the brain? Transient selection of subnetworks by metabotropic receptors and G protein-gated ion channels	6
Exploring the value of pleural fluid biomarkers for complementary pleural effusion disease examination	6
Exploring the interaction of phytochemicals from Hibiscus rosa-sinensis flowers with glucosidase and acetylcholinesterase: An integrated in vitro and in silico approach	6
GEHGAN: CircRNA–disease association prediction via graph embedding an	6
Acknowledgements to 2020 Reviewers	6
Harnessing the druggability at orthosteric and allosteric sites of PD-1 for small molecule discovery by an integrated in silico pipeline	6
Accelerating Long-Read Overlap Detection for Genome Assembly with a Two-Hash mTable Strategy	6
CTDN (Convolutional Temporal Based Deep‐ Neural Network): An Improvised Stacked Hybrid Computational Approach for Anticancer Drug Response Prediction	6
Cytokine expression patterns: A single-cell RNA sequencing and machine learning based roadmap for cancer classification	6
Planning biosynthetic pathways of target molecules based on metabolic reaction prediction and AND-OR tree search	6
Transfer learning with molecular graph convolutional networks for accurate modeling and representation of bioactivities of ligands targeting GPCRs without sufficient data	6