Computational Biology and Chemistry

Article	Citations
A comprehensive application: Molecular docking and network pharmacology for the prediction of bioactive constituents and elucidation of mechanisms of action in component-based Chinese medicine	121
Tuning hyperparameters of machine learning algorithms and deep neural networks using metaheuristics: A bioinformatics study on biomedical and biological cases	96
Synthesis, structural elucidation, DFT calculation, biological studies and DNA interaction of some aryl hydrazone Cr3+, Fe3+, and Cu2+ chelates	84
BERT-Promoter: An improved sequence-based predictor of DNA promoter using BERT pre-trained model and SHAP feature selection	58
A Recurrent Neural Network model to predict blood–brain barrier permeability	49
Interaction of small molecules with the SARS-CoV-2 main protease in silico and in vitro validation of potential lead compounds using an enzyme-linked immunosorbent assay	44
Exploration of the mechanism of Zisheng Shenqi decoction against gout arthritis using network pharmacology	41
Designing, characterization, biological, DFT, and molecular docking analysis for new FeAZD, NiAZD, and CuAZD complexes incorporating 1-(2-hydroxyphenylazo)− 2-naphthol (H2AZD)	34
A global report on the dynamics of COVID-19 with quarantine and hospitalization: A fractional order model with non-local kernel	33
Site mapping and small molecule blind docking reveal a possible target site on the SARS-CoV-2 main protease dimer interface	31
Identification of novel human USP2 inhibitor and its putative role in treatment of COVID-19 by inhibiting SARS-CoV-2 papain-like (PLpro) protease	30
Cholinesterases, carbonic anhydrase inhibitory properties and in silico studies of novel substituted benzylamines derived from dihydrochalcones	30
Alkylated benzimidazoles: Design, synthesis, docking, DFT analysis, ADMET property, molecular dynamics and activity against HIV and YFV	30
Atom counting method for determining elemental composition of viruses and its applications in biothermodynamics and environmental science	29
Efficient machine learning model for predicting drug-target interactions with case study for Covid-19	29
Genome-wide analysis of the MADS-Box gene family in Chrysanthemum	27
LMI-DForest: A deep forest model towards the prediction of lncRNA-miRNA interactions	27
Robust biomarker screening from gene expression data by stable machine learning-recursive feature elimination methods	25
Computational modeling of imines based anti-oxidant and anti-esterases compounds: Synthesis, single crystal and In-vitro assessment	25
lncRNA-miRNA-mRNA interaction network for colorectal cancer; An in silico analysis	24
Comprehensive analyses of bioinformatics applications in the fight against COVID-19 pandemic	24
Exploring of antioxidant and antibacterial properties of novel 1,3,4-thiadiazole derivatives: Facile synthesis, structural elucidation and DFT approach to antioxidant characteristics	24
Apache Spark based kernelized fuzzy clustering framework for single nucleotide polymorphism sequence analysis	23
Identification of human microRNA-disease association via hypergraph embedded bipartite local model	23
GanDTI: A multi-task neural network for drug-target interaction prediction	22

New naphthalene derivative for cost-effective AChE inhibitors for Alzheimer’s treatment: In silico identification, in vitro and in vivo validation	21
In silico virtual screening of potent inhibitor to hamper the interaction between HIV-1 integrase and LEDGF/p75 interaction using E-pharmacophore modeling, molecular docking, and dynamics simulations	21
MD-UNET: Multi-input dilated U-shape neural network for segmentation of bladder cancer	20
Bioinformatics analysis and verification of gene targets for renal clear cell carcinoma	20
The severity prediction of the binary and multi-class cardiovascular disease − A machine learning-based fusion approach	19
DeepAdd: Protein function prediction from k-mer embedding and additional features	19
Profiling the structural determinants of pyrrolidine derivative as gelatinases (MMP-2 and MMP-9) inhibitors using in silico approaches	19
Dual computational and biological assessment of some promising nucleoside analogs against the COVID-19-Omicron variant	19
Virtual screening using docking and molecular dynamics of cannabinoid analogs against CB1 and CB2 receptors	19
TAP 1.0: A robust immunoinformatic tool for the prediction of tumor T-cell antigens based on AAindex properties	18
In silico prediction of peptide variants from chia (S. hispanica L.) with antimicrobial, antibiofilm, and antioxidant potential	17
Enhancing the binding of the β-sheet breaker peptide LPFFD to the amyloid-β fibrils by aromatic modifications: A molecular dynamics simulation study	16
Amyloid β fibrils disruption by kolaviron: Molecular docking and extended molecular dynamics simulation studies	16
Design, synthesis, evaluation of new 3-acetylisoxazolines and their hybrid analogous as anticancer agents: In vitro and in silico analysis	16
ProS-GNN: Predicting effects of mutations on protein stability using graph neural networks	15
In silico and in vitro assessment of androgen receptor antagonists	15
Dissection of hubs and bottlenecks in a protein-protein interaction network	15
Physicochemical properties, drug likeness, ADMET, DFT studies, and in vitro antioxidant activity of oxindole derivatives	14
The reactivity of neurotransmitters and their metabolites towards various nitrogen-centered radicals: Experimental, theoretical, and biotoxicity evaluation	14
Design and various in silico studies of the novel curcumin derivatives as potential candidates against COVID-19 -associated main enzymes	14
Exploring enzyme inhibition profiles of novel halogenated chalcone derivatives on some metabolic enzymes: Synthesis, characterization and molecular modeling studies	14
Clinical significance of transcription factor RUNX2 in lung adenocarcinoma and its latent transcriptional regulating mechanism	13
The role of human C5a as a non-genomic target in corticosteroid therapy for management of severe COVID19	13
Early diagnosis of Parkinson’s disease: A combined method using deep learning and neuro-fuzzy techniques	13
Computational docking investigation of phytocompounds from bergamot essential oil against Serratia marcescens protease and FabI: Alternative pharmacological strategy	13
Identification of key genes of hesperidin in inhibition of breast cancer stem cells by functional network analysis	13
In silico design, synthesis and anti-HIV activity of quinoline derivatives as non-nucleoside reverse transcriptase inhibitors (NNRTIs)	13
Genetic analysis of SARS-CoV-2 isolates collected from Bangladesh: Insights into the origin, mutational spectrum and possible pathomechanism	13
A new approach for determining SARS-CoV-2 epitopes using machine learning-based in silico methods	13
Bisbenzylisoquinolines from Cissampelos pareira L. as antimalarial agents: Molecular docking, pharmacokinetics analysis, and molecular dynamic simulation studies	13
Design, semi-synthesis, anti-cancer assessment, docking, MD simulation, and DFT studies of novel theobromine-based derivatives as VEGFR-2 inhibitors and apoptosis inducers	12
Identification of novel vaccine candidates against carbapenem resistant Klebsiella pneumoniae: A systematic reverse proteomic approach	12
Exploiting reverse vaccinology approach for the design of a multiepitope subunit vaccine against the major SARS-CoV-2 variants	12
Virtual screening of dipeptidyl peptidase-4 inhibitors using quantitative structure–activity relationship-based artificial intelligence and molecular docking of hit compounds	12
Mathematical modeling and analysis of the SARS-Cov-2 disease with reinfection	12
Ensembling machine learning models to boost molecular affinity prediction	12
Molecular simulation studies to reveal the binding mechanisms of shikonin derivatives inhibiting VEGFR-2 kinase	11
Docking-based virtual screening studies aiming at the covalent inhibition of SARS-CoV-2 MPro by targeting the cysteine 145	11
Metaheuristics for multiple sequence alignment: A systematic review	11
Uncovering the pharmacological mechanism of motherwort (Leonurus japonicus Houtt.) for treating menstrual disorders: A systems pharmacology approach	11
Beyond standard pipeline and p < 0.05 in pathway enrichment analyses	10
ScGSLC: An unsupervised graph similarity learning framework for single-cell RNA-seq data clustering	10
In silico and in vitro studies of thiosemicarbazone-indole hybrid compounds as potent α-glycosidase inhibitors	10
Convolutional neural networks with image representation of amino acid sequences for protein function prediction	10
Discovery of potentially biased agonists of mu-opioid receptor (MOR) through molecular docking, pharmacophore modeling, and MD simulation	10
QSAR-based virtual screening of traditional Chinese medicine for the identification of mitotic kinesin Eg5 inhibitors	10
Machine learning prediction of 3CL SARS-CoV-2 docking scores	10
ABLE: Attention based learning for enzyme classification	10
Prediction of human-Streptococcus pneumoniae protein-protein interactions using logistic regression	9
Experimental and theoretical studies of Palladium-hydrazide complexes’ interaction with DNA and BSA, in vitro cytotoxicity activity and plasmid cleavage ability	9

Improved intelligent water drop-based hybrid feature selection method for microarray data processing	9
Structural protein fold recognition based on secondary structure and evolutionary information using machine learning algorithms	9
Lung cancer prediction using multi-gene genetic programming by selecting automatic features from amino acid sequences	9
Prediction for understanding the effectiveness of antiviral peptides	9
A computational study of non-coding RNAs on the regulation of activating transcription factor 3 in human breast cancer cells	9
Insights into binding molecular mechanism of hemagglutinin H3N2 of influenza virus complexed with arbidol and its derivative: A molecular dynamics simulation perspective	9
GGAECDA: Predicting circRNA-disease associations using graph autoencoder based on graph representation learning	9
Machine learning and molecular simulation ascertain antimicrobial peptide against Klebsiella pneumoniae from public database	9
L2,1-Extreme Learning Machine: An Efficient Robust Classifier for Tumor Classification	9
In silico analysis and characterization of medicinal mushroom cystathionine beta-synthase as an angiotensin converting enzyme (ACE) inhibitory protein	9
Discovering inhibitors of TEAD palmitate binding pocket through virtual screening and molecular dynamics simulation	9
Green synthesis of selenium based N-heterocyclic carbene compounds; structural, in-vitro anticancer and molecular docking studies	9
Computational identification of drug-like marine natural products as potential RNA polymerase inhibitors against Nipah virus	8
diSBPred: A machine learning based approach for disulfide bond prediction	8
PPred-PCKSM: A multi-layer predictor for identifying promoter and its variants using position based features	8
A computational essential dynamics approach to investigate structural influences of ligand binding on Papain like protease from SARS-CoV-2	8
Cerebral aneurysm evolution modeling from microstructural computational models to machine learning: A review	8
An ensemble learning framework for potential miRNA-disease association prediction with positive-unlabeled data	8
Identification of promising inhibitory heterocyclic compounds against acetylcholinesterase using QSAR, ADMET, biological activity, and molecular docking	8
Identifying the active compounds and mechanism of action of Banxia Xiexin decoction for treating ethanol-induced chronic gastritis using network pharmacology combined with UPLC–LTQ–Orbitrap MS	8
Design, DFT studies, antimicrobial and antioxidant potential of Binuclear N-heterocyclic Carbene (NHCs) complexes, Probing the aspect of DNA interaction through In-vitro and In-silico approach	8
Exploring the mechanism of Cremastra Appendiculata (SUANPANQI) against breast cancer by network pharmacology and molecular docking	8
Mutation-based Binary Aquila optimizer for gene selection in cancer classification	8
FPDock: Protein–protein docking using flower pollination algorithm	8
DeeProPre: A promoter predictor based on deep learning	8
Generative Pre-trained Transformer (GPT) based model with relative attention for de novo drug design	8
A multilevel approach for screening natural compounds as an antiviral agent for COVID-19	8
A survey on genomic data by privacy-preserving techniques perspective	8
Homotherapy for heteropathy active components and mechanisms of Qiang-Huo-Sheng-Shi decoction for treatment of rheumatoid arthritis and osteoarthritis	8
Instruction of molecular structure similarity and scaffolds of drugs under investigation in ebola virus treatment by atom-pair and graph network: A combination of favipiravir and molnupiravir	8
Peripheral blood mononuclear cell derived biomarker detection using eXplainable Artificial Intelligence (XAI) provides better diagnosis of breast cancer	8
A comprehensive in Silico analysis of the functional and structural impact of single nucleotide polymorphisms (SNPs) in the human IL-33 gene	8
Cellular and molecular level host-pathogen interactions in Francisella tularensis: A microbial gene network study	8
T-A-MFFNet: Multi-feature fusion network for EEG analysis and driving fatigue detection based on time domain network and attention network	8
A meta-analysis of tumor necrosis factor (TNF) gene polymorphism and susceptibility to influenza A (H1N1)	7
SE-BLTCNN: A channel attention adapted deep learning model based on PSSM for membrane protein classification	7
ActTRANS: Functional classification in active transport proteins based on transfer learning and contextual representations	7
Elucidation of partial activation of cannabinoid receptor type 2 and identification of potential partial agonists: Molecular dynamics simulation and structure-based virtual screening	7
LPI-CSFFR: Combining serial fusion with feature reuse for predicting LncRNA-protein interactions	7
Deep_CNN_LSTM_GO: Protein function prediction from amino-acid sequences	7
Extraction of knowledge graph of Covid-19 through mining of unstructured biomedical corpora	7
Deep protein representations enable recombinant protein expression prediction	7
In vitro and in silico evaluation of new thieno[2,3-d]pyrimidines as anti-cancer agents and apoptosis inducers targeting VEGFR-2	7
A tag based joint extraction model for Chinese medical text	7
Design, synthesis, molecular dynamics simulation, MM/GBSA studies and kinesin spindle protein inhibitory evaluation of some 4-aminoquinoline hybrids	7
Transcription factors and chaperone proteins play a role in launching a faster response to heat stress and aggregation	7
Developing new PI3Kγ inhibitors by combining pharmacophore modeling, molecular dynamic simulation, molecular docking, fragment-based drug design, and virtual screening	7
MinimapR: A parallel alignment tool for the analysis of large-scale third-generation sequencing data	7
Polymorphic landscape of SARS-CoV-2 genomes isolated from Indian population in 2020 demonstrates rapid evolution in ORF3a, ORF8, nucleocapsid phosphoprotein and spike glycoprotein	7
The Wnt pathway can stabilize hybrid phenotypes in the epithelial-mesenchymal transition: A logical modeling approach	7
Discovery of small-molecule PD-1/PD-L1 antagonists through combined virtual screening and experimental validation	7
Design and In-silico study of bioimaging fluorescence Graphene quantum dot-Bovine serum albumin complex synthesized by diimide-activated amidation	7
Molecular dynamic simulation analysis of SARS-CoV-2 spike mutations and evaluation of ACE2 from pets and wild animals for infection risk	7
Discovery of potential inhibitors targeting the kinase domain of polynucleotide kinase/phosphatase (PNKP): Homology modeling, virtual screening based on multiple conformations, and molecular dynamics	7
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	7
HADEG: A curated hydrocarbon aerobic degradation enzymes and genes database	7
Computational analysis revealed miRNAs produced by Chikungunya virus target genes associated with antiviral immune responses and cell cycle regulation	7
North East India medicinal plants database (NEI-MPDB)	7
Transboundary Pathogenic microRNA Analysis Framework for Crop Fungi Driven by Biological Big Data and Artificial Intelligence Model	7
MiR-330-3p and miR-485-5p as biomarkers for glioblastoma: An integrated bioinformatics and experimental study	7
Design, synthesis, characterization, in vitro cytotoxic, antimicrobial, antioxidant studies, DFT, thermal and molecular docking evaluation of biocompatible Co(II) complexes of N4O4-macrocyclic ligands	7
ChromosomeNet: A massive dataset enabling benchmarking and building basedlines of clinical chromosome classification	7
Modelling the spread of covid-19 in the capital of Brazil using numerical solution and cellular automata	7
Structure-based virtual screening for novel potential selective inhibitors of class IIa histone deacetylases for cancer treatment	7
iR5hmcSC: Identifying RNA 5-hydroxymethylcytosine with multiple features based on stacking learning	6
Design, synthesis, In-vitro, In-silico and DFT studies of novel functionalized isoxazoles as antibacterial and antioxidant agents	6
Structure-based virtual screening of dipeptidyl peptidase 4 inhibitors and their in vitro analysis	6
MMDAE-HGSOC: A novel method for high-grade serous ovarian cancer molecular subtypes classification based on multi-modal deep autoencoder	6
Drug repurposing for Basal breast cancer subpopulations using modular network signatures	6
m6A-Finder: Detecting m6A methylation sites from RNA transcriptomes using physical and statistical properties based features	6
Exploring antiviral potency of N-1 substituted pyrimidines against HIV-1 and other DNA/RNA viruses: Design, synthesis, characterization, ADMET analysis, docking, molecular dynamics and biological acti	6
Computational study and design of effective siRNAs to silence structural proteins associated genes of Indian SARS-CoV-2 strains	6
A network-based pharmacology study of active compounds and targets of Fritillaria thunbergii against influenza	6
Forcefield evaluation and accelerated molecular dynamics simulation of Zn(II) binding to N-terminus of amyloid-β	6
The RIT1 C-terminus associates with lipid bilayers via charge complementarity	6
PmiRtarbase: A positive miRNA-target regulations database	6
Visualization of UV and ECD spectra of E&Z isomers of N-(4′-Hydroxy-cinnamoyl)− 5- hydroxyanthranilic acid	6
Phytotoxic property of metabolites isolated from Garcinia gardneriana	6
1,3-Oxazole derivatives of cytisine as potential inhibitors of glutathione reductase of Candida spp.: QSAR modeling, docking analysis and experimental study of new anti-Candida agents	6
OSADHI – An online structural and analytics based database for herbs of India	6

Integrated structure-guided computational design of novel substituted quinolizin-4-ones as Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors	6
Protein complex prediction in interaction network based on network motif	6
Potential Achilles heels of SARS-CoV-2 are best displayed by the base order-dependent component of RNA folding energy	6
Named entity recognition of rice genes and phenotypes based on BiGRU neural networks	6
The regulation of microRNA in each of cancer stage from two different ethnicities as potential biomarker for breast cancer	6
Natural selection shaped the evolution of amino acid usage in mammalian toll like receptor genes	6
Drug repurposing for hyperlipidemia associated disorders: An integrative network biology and machine learning approach	5
SubFeat: Feature subspacing ensemble classifier for function prediction of DNA, RNA and protein sequences	5
HR-LCMS and evaluation of anti-diabetic activity of Hemidesmus indicus (anantmool): Kinetic study, and molecular modelling approach	5
A promising in silico protocol to develop novel PPARγ antagonists as potential anticancer agents: Design, synthesis and experimental validation via PPARγ protein activity and competitive binding assay	5
Designing of thiazolidinones against chicken pox, monkey pox, and hepatitis viruses: A computational approach	5
Design, synthesis, antibacterial evaluation, molecular docking and computational study of 4-alkoxy/aryloxyphenyl cyclopropyl methane oxime derivatives	5
BCM-DTI: A fragment-oriented method for drug–target interaction prediction using deep learning	5
Competition between Ag+ and Ni2+ in nickel enzymes: Implications for the Ag+ antibacterial activity	5
The marijuana-schizophrenia multifaceted nexus: Connections and conundrums towards neurophysiology	5
Designing potential siRNA molecule for the nucleocapsid(N) gene silencing of different SARS-CoV-2 strains of Bangladesh: Computational approach	5
BAT-Net: An enhanced RNA Secondary Structure prediction via bidirectional GRU-based network with attention mechanism	5
EBOLApred: A machine learning-based web application for predicting cell entry inhibitors of the Ebola virus	5
Inference of gene regulatory networks based on the Light Gradient Boosting Machine	5
Protein sequence profile prediction using ProtAlbert transformer	5
DTIP-TC2A: An analytical framework for drug-target interactions prediction methods	5
In-silico analysis of non-synonymous single nucleotide polymorphisms in human β-defensin type 1 gene reveals their impact on protein-ligand binding sites	5
Identification of novel efflux pump inhibitors for Neisseria gonorrhoeae via multiple ligand-based pharmacophores, e-pharmacophore, molecular docking, density functional theory, and molecular dynamics	5
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)	5
Predictive modeling of antibacterial activity of ionic liquids by machine learning methods	5
Mutation in Eth A protein of Mycobacterium tuberculosis conferred drug tolerance against enthinoamide in Mycobacterium smegmatis mc2155	5
Integrated computational approaches for designing potent pyrimidine-based CDK9 inhibitors: 3D-QSAR, docking, and molecular dynamics simulations	5
Integrated transcriptomics and proteomics data analysis identifies CDH17 as a key cell surface target in colorectal cancer	5
BRWMC: Predicting lncRNA-disease associations based on bi-random walk and matrix completion on disease and lncRNA networks	5
Down regulation of lactotransferrin enhanced radio-sensitivity of nasopharyngeal carcinoma	5
Cell-based assays and molecular simulation reveal that the anti-cancer harmine is a specific matrix metalloproteinase-3 (MMP-3) inhibitor	5
A hybrid ensemble and evolutionary algorithm for imbalanced classification and its application on bioinformatics	5
Bipartite molecular approach for species delimitation and resolving cryptic speciation of Exobasidium vexans within the Exobasidium genus	5
ICTC-RAAC: An improved web predictor for identifying the types of ion channel-targeted conotoxins by using reduced amino acid cluster descriptors	5
SENet: A deep learning framework for discriminating super- and typical enhancers by sequence information	5