Computational Biology and Chemistry

Article	Citations
Integrated consensus genetic map and genomic scaffold re-ordering of oil palm (Elaeis guineensis) genome	139
Decision tree classifier based on topological characteristics of subgraph for the mining of protein complexes from large scale PPI networks	101
The interaction of methotrexate with the human C5a and its potential therapeutic implications	72
Construction of the small intestine on molecular dynamics simulation and preliminary exploration of drug intestinal absorption prediction	47
Computational investigations of indanedione and indanone derivatives in drug discovery: Indanone derivatives inhibits cereblon, an E3 ubiquitin ligase component	43
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	40
Editorial Board	37
Editorial Board	34
Editorial Board	33
Multi-scale DNA language model improves 6 mA binding sites prediction	30
Identification of angiogenesis-related subtypes and risk models for predicting the prognosis of gastric cancer patients	30
Computational insights into irinotecan's interaction with UBE2I in ovarian and endometrial cancers	30
A novel parallel feature rank aggregation algorithm for gene selection applied to microarray data classification	29
Prediction of human-Streptococcus pneumoniae protein-protein interactions using logistic regression	28
Computational analysis of the interactions between Ebselen and derivatives with the active site of the main protease from SARS-CoV-2	26
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	25
Implications of trinodal inhibitions and drug repurposing in MAPK pathway: A putative remedy for breast cancer	25
Classical molecular dynamics simulation identifies catechingallate as a promising antiviral polyphenol against MPOX palmitoylated surface protein	25
Editorial Board	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	24
Integrated regulatory network based on lncRNA-miRNA-mRNA-TF reveals key genes and sub-networks associated with dilated cardiomyopathy	24
Comprehensive analyses of bioinformatics applications in the fight against COVID-19 pandemic	24
Molecular insights into the mechanism of sugar-modified enkephalin binding to opioid receptors	24
Bioinformatics analysis and verification of gene targets for renal clear cell carcinoma	23

A global report on the dynamics of COVID-19 with quarantine and hospitalization: A fractional order model with non-local kernel	23
Interactions between DNA and the acridine intercalator: A computational study	23
Integrated structure-guided computational design of novel substituted quinolizin-4-ones as Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors	22
MSFF-MA-DDI: Multi-Source Feature Fusion with Multiple Attention blocks for predicting Drug–Drug Interaction events	22
SNSynergy: Similarity network-based machine learning framework for synergy prediction towards new cell lines and new anticancer drug combinations	21
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	19
Exploration of functional relations among differentially co-expressed genes identifies regulators in glioblastoma	19
Thiazole inhibitors of α-glucosidase: Positional isomerism modulates selectivity, enzyme binding and potency of inhibition	18
Computational analyses of the interactome between TNF and TNFR superfamilies	18
Exploring the effectiveness of the TSR-based protein 3-D structural comparison method for protein clustering, and structural motif identification and discovery of protein kinases, hydrolases, and SARS	18
Bisbenzylisoquinolines from Cissampelos pareira L. as antimalarial agents: Molecular docking, pharmacokinetics analysis, and molecular dynamic simulation studies	18
Exploring fingerprints for antidiabetic therapeutics related to peroxisome proliferator-activated receptor gamma (PPARγ) modulators: A chemometric modeling approach	18
SSA: Subset sum approach to protein β-sheet structure prediction	17
STRIDER: Steric hindrance and metal coordination identifier	17
Identification of calcineurin as a predictor of oocyte quality and fertilization competence based on microarray data	17
Impact of calcium ions on the structural and dynamic properties of heparin oligosaccharides by computational analysis	17
Tensor improve equivariant graph neural network for molecular dynamics prediction	16
MD-UNET: Multi-input dilated U-shape neural network for segmentation of bladder cancer	16
Amyloid β fibrils disruption by kolaviron: Molecular docking and extended molecular dynamics simulation studies	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	16
An efficient new method of ytterbium(III) triflate catalysis approach to the synthesis of substituted pyrroles: DFT, ADMET, and molecular docking investigations	16
An assessment of crucial structural contributors of HDAC6 inhibitors through fragment-based non-linear pattern recognition and molecular dynamics simulation approaches	16
BAT-Net: An enhanced RNA Secondary Structure prediction via bidirectional GRU-based network with attention mechanism	16
Vector embeddings by sequence similarity and context for improved compression, similarity search, clustering, organization, and manipulation of cDNA libraries	15
Comparative in Silico study of apigenin and its dimeric forms on PIM1 kinase in glioblastoma multiform	15
FusPB-ESM2: Fusion model of ProtBERT and ESM-2 for cell-penetrating peptide prediction	15
Gene-expression profile analysis to disclose diagnostics and therapeutics biomarkers for thyroid carcinoma	15
Classification and prediction of variants associated with hearing loss using sequence information in the vicinity of mutation sites	14
GAP positions catalytic H-Ras residue Q61 for GTP hydrolysis in molecular dynamics simulations, complicating chemical rescue of Ras deactivation	14
Catalytic activity in vitro of the human protein kinase ASK1 mutants: Experimental and molecular simulation study	14
Machine learning approaches for predicting craniofacial anomalies with graph neural networks	14
Reliable estrogen-related prognostic signature for uterine corpus endometrial carcinoma	14
P-FARFAR2: A multithreaded greedy approach to sampling low-energy RNA structures in Rosetta FARFAR2	14
An ensemble of bioinformatics and machine learning approaches to identify shared breast cancer biomarkers among diverse populations	14
Graph-ETMB: A graph neural network-based model for tumour mutation burden estimation	13
SME-MFP: A novel spatiotemporal neural network with multiangle initialization embedding toward multifunctional peptides prediction	13
Targeting AR-positive breast cancer cells via drug repurposing approach	13
Metaheuristics for multiple sequence alignment: A systematic review	13
CopyMix: Mixture model based single-cell clustering and copy number profiling using variational inference	13
Editorial Board	12
Deep protein representations enable recombinant protein expression prediction	12
Editorial	12
A comprehensive investigation regarding the clinical significance of ITGB4 in oral squamous cell carcinoma combining immunohistochemistry, RNA-seq, and microarray data	12
Modelling the transport mechanism of organic molecules into cell membranes: The role of organic solvents	12
Apache Spark based kernelized fuzzy clustering framework for single nucleotide polymorphism sequence analysis	11
Computational analysis of substrate recognition of Sars-Cov-2 Mpro main protease	11
Editorial Board	11
An assembling strategy for DNA cages with minimum strands	11
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)	11

Human drug-pathway association prediction based on network consistency projection	11
Discovery of small-molecule PD-1/PD-L1 antagonists through combined virtual screening and experimental validation	11
Transcriptome analysis reveals mechanisms of metabolic detoxification and immune responses following farnesyl acetate treatment in Metisa plana	11
UmamiPreDL: Deep learning model for umami taste prediction of peptides using BERT and CNN	10
A computational essential dynamics approach to investigate structural influences of ligand binding on Papain like protease from SARS-CoV-2	10
Machine learning and molecular subtyping reveal the impact of diverse patterns of cell death on the prognosis and treatment of hepatocellular carcinoma	10
A composite ranking of risk factors for COVID-19 time-to-event data from a Turkish cohort	10
Deep2Pep: A Deep Learning Method in Multi-label Classification of Bioactive Peptide	10
Integrated deep learning model for automatic detection and classification of stenosis in coronary angiography	10
scDGG: Dynamic Gene Graphs for enhancing spatial and temporal analysis of single-cell RNA sequencing data	10
The marijuana-schizophrenia multifaceted nexus: Connections and conundrums towards neurophysiology	10
Identification of phytoestrogens as sirtuin inhibitor against breast cancer: Multitargeted approach	10
Fractional whale driving training-based optimization enabled transfer learning for detecting autism spectrum disorder	10
Computational exploration of Ganoderma lucidum metabolites as potential anti-atherosclerotic agents: Insights from molecular docking and dynamics simulations	10
Synthesis, structural elucidation, DFT calculation, biological studies and DNA interaction of some aryl hydrazone Cr3+, Fe3+, and Cu2+ chelates	10
A computational analysis of molecular evolution for virulence genes of zoonotic novel coronavirus (COVID-19)	9
MMR: A Multi-view Merge Representation model for Chemical-Disease relation extraction	9
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	9
ACDMBI: A deep learning model based on community division and multi-source biological information fusion predicts essential proteins	9
Antihyperlipidemic mechanisms of a formula containing Curcuma xanthorrhiza, Sechium edule, and Syzigium polyanthum: In silico and in vitro studies	9
Towards development of new antimalarial compounds through in silico and in vitro assays	9
CNVABNN: An AdaBoost algorithm and neural networks-based detection of copy number variations from NGS data	9
LPI-CSFFR: Combining serial fusion with feature reuse for predicting LncRNA-protein interactions	9
Integrating multiple sequence features for identifying anticancer peptides	9
Identifying potential Alzheimer's disease therapeutics through GSK-3β inhibition: A molecular docking and dynamics approach	9
Osmotic pressure induced by extracellular matrix drives Bacillus subtilis biofilms' self-healing	9
ANNInter: A platform to explore ncRNA-ncRNA interactome of Arabidopsis thaliana	9
Using a dual immunoinformatics and bioinformatics approach to design a novel and effective multi-epitope vaccine against human torovirus disease	9
Chemogenomic approach to identifying nematode chemoreceptor drug targets in the entomopathogenic nematode Heterorhabditis bacteriophora	9
Editorial Board	9
Acknowledgements to 2019 Reviewers	8
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)	8
In silico profiling, docking analysis, and protein interactions of secondary metabolites in Musa spp. Against the SGE1 protein of Fusarium oxysporum f. sp. cubense	8
Enhancing gene regulatory networks inference through hub-based data integration	8
ACP-ESM2: The prediction of anticancer peptides based on pre-trained classifier	8
Designing, characterization, biological, DFT, and molecular docking analysis for new FeAZD, NiAZD, and CuAZD complexes incorporating 1-(2-hydroxyphenylazo)− 2-naphthol (H2AZD)	8
ActTRANS: Functional classification in active transport proteins based on transfer learning and contextual representations	8
Role of surface-exposed charged basic amino acids (Lys, Arg) and guanidination in insulin on the interaction and stability of insulin–insulin receptor complex	8
Computational analysis revealed miRNAs produced by Chikungunya virus target genes associated with antiviral immune responses and cell cycle regulation	8
A Boolean model of the oncogene role of FAM111B in lung adenocarcinoma	8
TopMarker: Computational screening biomarkers of hepatocellular carcinoma from transcriptome and interactome based on differential network topological parameters	8
Dual computational and biological assessment of some promising nucleoside analogs against the COVID-19-Omicron variant	8
Identification and validation of miR-21 key genes in cervical cancer through an integrated bioinformatics approach	8
Correlation intensity index-index of ideality of correlation: A hyphenated target function for furtherance of MAO-B inhibitory activity assessment	8
Statistical analysis of the unique characteristics of secondary structures in proteins	8
In silico exploration of CB2 receptor agonist in the management of neuroinflammatory conditions by pharmacophore modeling	7
Transcription factors and chaperone proteins play a role in launching a faster response to heat stress and aggregation	7
Designing of thiazolidinones against chicken pox, monkey pox, and hepatitis viruses: A computational approach	7
Intrinsic relative preference profile of pan-kinase inhibitor drug staurosporine towards the clinically occurring gatekeeper mutations in Protein Tyrosine Kinases	7
Integrated in silico and experimental discovery of trimeric peptide ligands targeting Butyrylcholinesterase	7
A structure-based approach to discover a potential isomerase Pin1 inhibitor for cancer therapy using computational simulation and biological studies	7
Investigating Lycotoxin-An1a (An1a), a defense antiviral peptide from Alopecosa nagpag venom as prospective anti-dengue agent against DENV-2 NS2B-NS3 protease	7
Exploring of antioxidant and antibacterial properties of novel 1,3,4-thiadiazole derivatives: Facile synthesis, structural elucidation and DFT approach to antioxidant characteristics	7
Exploring potential molecular targets and therapeutic efficacy of beauvericin in triple-negative breast cancer cells	7
Mining channel-regulated peptides from animal venom by integrating sequence semantics and structural information	7
Integrative bioinformatics analysis of immune activation and gene networks in pediatric septic arthritis	7
Editorial Board	7
Novel 1,4 benzothiazine 3-one derivatives as anticonvulsant agents: Design, synthesis, biological evaluation and computational studies	7
Robust biomarker screening from gene expression data by stable machine learning-recursive feature elimination methods	7
The prevalence of dementia in humans could be the result of a functional adaptation	7
DeepOCR: A multi-species deep-learning framework for accurate identification of open chromatin regions in livestock	7
Rational design of antimicrobial peptides targeting Gram-negative bacteria	7
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	7
Prediction of protein structural class based on symmetrical recurrence quantification analysis	7
Machine learning and molecular simulation ascertain antimicrobial peptide against Klebsiella pneumoniae from public database	7
A deep-SIQRV epidemic model for COVID-19 to access the impact of prevention and control measures	7
Cancer detection with various classification models: A comprehensive feature analysis using HMM to extract a nucleotide pattern	7
Exploring casual effects and shared molecular mechanism between psoriasis and liver cancer through Mendelian randomization and comprehensive bioinformatic analyses	7
Exploring enzyme inhibition profiles of novel halogenated chalcone derivatives on some metabolic enzymes: Synthesis, characterization and molecular modeling studies	7
Green synthesis of selenium based N-heterocyclic carbene compounds; structural, in-vitro anticancer and molecular docking studies	7
SE-BLTCNN: A channel attention adapted deep learning model based on PSSM for membrane protein classification	7
16S amplicon sequencing and functional gene prediction of microbial community in Inner West Aegean, Turkey	7
Investigating pH-induced conformational switch in PIM-1: An integrated multi spectroscopic and MD simulation study	7
Prognostic significance of a 3-gene ferroptosis-related signature in lung cancer via LASSO analysis and cellular functions of UBE2Z	7
Visualization of UV and ECD spectra of E&Z isomers of N-(4′-Hydroxy-cinnamoyl)− 5- hydroxyanthranilic acid	7
Unveiling novel type 1 inhibitors for targeting LIM kinase 2 (LIMK2) for cancer therapeutics: An integrative pharmacoinformatics approach	7
Investigation of dual inhibition of antibacterial and antiarthritic drug candidates using combined approach including molecular dynamics, docking and quantum chemical methods	7
Co-expression network and survival analysis of breast cancer inflammation and immune system hallmark genes	7
ARGai 1.0: A GAN augmented in silico approach for identifying resistant genes and strains in E. coli using vision transformer	6
Uncovering the antidiabetic potential of heart-friendly and diuretic bioactive compounds through computer-based drug design	6

Design, synthesis, In-vitro, In-silico and DFT studies of novel functionalized isoxazoles as antibacterial and antioxidant agents	6
Reconstruction of the binding pathway of an anti-HIV drug, Indinavir, in complex with the HTLV-1 protease using unaggregated unbiased molecular dynamics simulation	6
Virtual screening of polyherbal compounds for AKT1 and HSPB1 inhibition in breast cancer apoptosis pathway	6
Screening of the effective sites of Cichorium glandulosum against hyperuricemia combined with hyperlipidemia and its network pharmacology analysis	6
Multiscale modeling of the cellular uptake of C6 peptide-siRNA complexes	6
IoT based healthcare system using fractional dung beetle optimization enabled deep learning for breast cancer classification	6
Theoretical Investigations of a point mutation affecting H5 Hemagglutinin’s receptor binding preference	6
Encoding the space of protein-protein binding interfaces by artificial intelligence	6
Halting aberrant DNA methylation via in silico Identification of potent inhibitors of DNMT3B enzyme: Atomistic insights	6
Integrated computational approaches for designing potent pyrimidine-based CDK9 inhibitors: 3D-QSAR, docking, and molecular dynamics simulations	6
Real-to-bin conversion for protein residue distances	6
An open source in silico workflow to assist in the design of fusion proteins	6
In silico analysis and prediction of transcription factors of the proteins interacting with astrocyte elevated gene-1	6
Acknowledgements to 2020 Reviewers	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
Cellular and molecular level host-pathogen interactions in Francisella tularensis: A microbial gene network study	6
Pharmacoinformatics-based prediction of Checkpoint kinase-1 inhibitors from Momordica charantia Linn. for cancer	6
K1K2NN: A novel multi-label classification approach based on neighbors for predicting COVID-19 drug side effects	6
Molecular dynamic simulation analysis of SARS-CoV-2 spike mutations and evaluation of ACE2 from pets and wild animals for infection risk	6
Ensembling machine learning models to boost molecular affinity prediction	6
The method predicting interaction between protein targets and small-molecular ligands with the wide applicability domain	6
Harnessing the druggability at orthosteric and allosteric sites of PD-1 for small molecule discovery by an integrated in silico pipeline	6
Design and characterization of defined alpha-helix mini-proteins with intrinsic cell permeability	5
A novel prognostic risk score model based on RNA editing level in lower-grade glioma	5
Editorial Board	5
Targeting cyclin-dependent kinase 2 CDK2: Insights from molecular docking and dynamics simulation – A systematic computational approach to discover novel cancer therapeutics	5
Vaginal birth after cesarean section prediction model for Jordanian population	5
Where is the mind within the brain? Transient selection of subnetworks by metabotropic receptors and G protein-gated ion channels	5
N-glycosylation reinforces interaction of immune checkpoint TIM-3 with a small molecule ligand	5
Design and In-silico study of bioimaging fluorescence Graphene quantum dot-Bovine serum albumin complex synthesized by diimide-activated amidation	5
FPDock: Protein–protein docking using flower pollination algorithm	5
Comments on 'Flexibility of enzymatic transitions as a hallmark of optimized enzyme steady-state kinetics and thermodynamics'	5
Non-homogeneous Poisson and renewal processes as spatial models for cancer mutation	5
Exploring the interaction of phytochemicals from Hibiscus rosa-sinensis flowers with glucosidase and acetylcholinesterase: An integrated in vitro and in silico approach	5
In silico identification of candidate miRNA-encoded Peptides in four Fabaceae species	5
Non-kin selection enhances complexity in cooperation: A unified quantitative law	5
Halogenated class of oximes as a new class of monoamine oxidase-B inhibitors for the treatment of Parkinson’s disease: Synthesis, biochemistry, and molecular dynamics study	5
Efficient assembly consensus algorithms for divergent contig sets	5
Editorial Board	5
Terpenoid phytocompounds from mangrove plant Xylocarpus moluccensis as possible inhibitors against SARS-CoV-2: In silico strategy	5
Protein function prediction using functional inter-relationship	5
Computational study and design of effective siRNAs to silence structural proteins associated genes of Indian SARS-CoV-2 strains	5
Cytokine expression patterns: A single-cell RNA sequencing and machine learning based roadmap for cancer classification	5
DeepRHD: An efficient hybrid feature extraction technique for protein remote homology detection using deep learning strategies	5
Exploring the value of pleural fluid biomarkers for complementary pleural effusion disease examination	5
Convolutional neural networks with image representation of amino acid sequences for protein function prediction	5
Integrating classic AI and agriculture: A novel model for predicting insecticide-likeness to enhance efficiency in insecticide development	5
CTDN (Convolutional Temporal Based Deep‐ Neural Network): An Improvised Stacked Hybrid Computational Approach for Anticancer Drug Response Prediction	5
Glycosylation is key for enhancing drug recognition into spike glycoprotein of SARS-CoV-2	5
OTUCD: Unsupervised GCN based metagenomics non-overlapping community detection	5
Bipartite molecular approach for species delimitation and resolving cryptic speciation of Exobasidium vexans within the Exobasidium genus	5
Sub-structure-based screening and molecular docking studies of potential enteroviruses inhibitors	5
Profiling the structural determinants of pyrrolidine derivative as gelatinases (MMP-2 and MMP-9) inhibitors using in silico approaches	5
Transfer learning with molecular graph convolutional networks for accurate modeling and representation of bioactivities of ligands targeting GPCRs without sufficient data	5
Advancing Drug-Target Interaction prediction with BERT and subsequence embedding	5
Differentiating stable and unstable protein using convolution neural network and molecular dynamics simulations	5
An efficient Burrows–Wheeler transform-based aligner for short read mapping	5
ETENLNC: An end to end lncRNA identification and analysis framework to facilitate construction of known and novel lncRNA regulatory networks	5
TSSUNet-MB – ab initio identification of σ70 promoter transcription start sites in Escherichia coli using deep multitask learning	5
Ligand binding free energy evaluation by Monte Carlo Recursion	5
Planning biosynthetic pathways of target molecules based on metabolic reaction prediction and AND-OR tree search	5
GEHGAN: CircRNA–disease association prediction via graph embedding an	5
Effects of 1,4-dihydropyridine derivatives on cell injury and mTOR of HepG2 and 3D-QSAR study	5