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	103
Geo-Measures: A PyMOL plugin for protein structure ensembles analysis	87
Spectroscopic elucidation (FT-IR, FT-Raman and UV-visible) with NBO, NLO, ELF, LOL, drug likeness and molecular docking analysis on 1-(2-ethylsulfonylethyl)-2-methyl-5-nitro-imidazole: An antiprotozoa	80
Synthesis, structural elucidation, DFT calculation, biological studies and DNA interaction of some aryl hydrazone Cr3+, Fe3+, and Cu2+ chelates	71
Tuning hyperparameters of machine learning algorithms and deep neural networks using metaheuristics: A bioinformatics study on biomedical and biological cases	70
Virtual screening of approved drugs as potential SARS-CoV-2 main protease inhibitors	61
Molecular docking studies, structural and spectroscopic properties of monomeric and dimeric species of benzofuran-carboxylic acids derivatives: DFT calculations and biological activities	61
Incorporating deep learning and multi-omics autoencoding for analysis of lung adenocarcinoma prognostication	57
A deep learning approach based on convolutional LSTM for detecting diabetes	56
Repurposing approved drugs as potential inhibitors of 3CL-protease of SARS-CoV-2: Virtual screening and structure based drug design	54
BERT-Promoter: An improved sequence-based predictor of DNA promoter using BERT pre-trained model and SHAP feature selection	49
Design, molecular docking analysis of an anti-inflammatory drug, computational analysis and intermolecular interactions energy studies of 1-benzothiophene-2-carboxylic acid	49
Interaction of the prototypical α-ketoamide inhibitor with the SARS-CoV-2 main protease active site in silico: Molecular dynamic simulations highlight the stability of the ligand-protein complex	48
A Recurrent Neural Network model to predict blood–brain barrier permeability	44
Inferring LncRNA-disease associations based on graph autoencoder matrix completion	42
SETE: Sequence-based Ensemble learning approach for TCR Epitope binding prediction	42
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	41
Computational study of 3-thiophene acetic acid: Molecular docking, electronic and intermolecular interactions investigations	38
Protein kinase inhibitors’ classification using K-Nearest neighbor algorithm	33
Exploration of the mechanism of Zisheng Shenqi decoction against gout arthritis using network pharmacology	33
In silico modeling for dual inhibition of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) enzymes in Alzheimer’s disease	32
Network pharmacology analysis of Chaihu Lizhong Tang treating non-alcoholic fatty liver disease	31
A global report on the dynamics of COVID-19 with quarantine and hospitalization: A fractional order model with non-local kernel	30
Site mapping and small molecule blind docking reveal a possible target site on the SARS-CoV-2 main protease dimer interface	30
hERG-Att: Self-attention-based deep neural network for predicting hERG blockers	29

Identification of novel human USP2 inhibitor and its putative role in treatment of COVID-19 by inhibiting SARS-CoV-2 papain-like (PLpro) protease	29
Atom counting method for determining elemental composition of viruses and its applications in biothermodynamics and environmental science	28
Efficient machine learning model for predicting drug-target interactions with case study for Covid-19	27
Theoretical analysis of bacterial efflux pumps inhibitors: Strategies in-search of competent molecules and develop next	26
An in-silico approach to study the possible interactions of miRNA between human and SARS-CoV2	26
Designing, characterization, biological, DFT, and molecular docking analysis for new FeAZD, NiAZD, and CuAZD complexes incorporating 1-(2-hydroxyphenylazo)− 2-naphthol (H2AZD)	25
ncRDeep: Non-coding RNA classification with convolutional neural network	25
Genome-wide analysis of the MADS-Box gene family in Chrysanthemum	25
Cholinesterases, carbonic anhydrase inhibitory properties and in silico studies of novel substituted benzylamines derived from dihydrochalcones	25
LMI-DForest: A deep forest model towards the prediction of lncRNA-miRNA interactions	25
lncRNA-miRNA-mRNA interaction network for colorectal cancer; An in silico analysis	24
Alkylated benzimidazoles: Design, synthesis, docking, DFT analysis, ADMET property, molecular dynamics and activity against HIV and YFV	24
Predicting novel CircRNA-disease associations based on random walk and logistic regression model	23
A machine learning approach to select features important to stroke prognosis	23
Swarm intelligence based clustering technique for automated lesion detection and diagnosis of psoriasis	22
Apache Spark based kernelized fuzzy clustering framework for single nucleotide polymorphism sequence analysis	22
Identification of human microRNA-disease association via hypergraph embedded bipartite local model	21
Gene structure, evolution and expression analysis of the P-ATPase gene family in Chinese pear (Pyrus bretschneideri)	21
Exploring of antioxidant and antibacterial properties of novel 1,3,4-thiadiazole derivatives: Facile synthesis, structural elucidation and DFT approach to antioxidant characteristics	20
Comprehensive analyses of bioinformatics applications in the fight against COVID-19 pandemic	20
Improved neural networks based on genetic algorithm for pulse recognition	20
New naphthalene derivative for cost-effective AChE inhibitors for Alzheimer’s treatment: In silico identification, in vitro and in vivo validation	20
GanDTI: A multi-task neural network for drug-target interaction prediction	19
CWLy-SVM: A support vector machine-based tool for identifying cell wall lytic enzymes	18
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	18
Profiling the structural determinants of pyrrolidine derivative as gelatinases (MMP-2 and MMP-9) inhibitors using in silico approaches	17
iPiDA-sHN: Identification of Piwi-interacting RNA-disease associations by selecting high quality negative samples	17
Dual computational and biological assessment of some promising nucleoside analogs against the COVID-19-Omicron variant	16
Identification of potential inhibitors of human methionine aminopeptidase (type II) for cancer therapy: Structure-based virtual screening, ADMET prediction and molecular dynamics studies	16
A DFT study on the metal ion selectivity of deferiprone complexes	16
MD-UNET: Multi-input dilated U-shape neural network for segmentation of bladder cancer	16
The severity prediction of the binary and multi-class cardiovascular disease − A machine learning-based fusion approach	16
DeepAdd: Protein function prediction from k-mer embedding and additional features	16
A review of Cloud computing technologies for comprehensive microRNA analyses	15
TAP 1.0: A robust immunoinformatic tool for the prediction of tumor T-cell antigens based on AAindex properties	15
In silico and in vitro assessment of androgen receptor antagonists	15
Virtual screening using docking and molecular dynamics of cannabinoid analogs against CB1 and CB2 receptors	15
Computational modeling of imines based anti-oxidant and anti-esterases compounds: Synthesis, single crystal and In-vitro assessment	15
Bioinformatics analysis and verification of gene targets for renal clear cell carcinoma	15
Robust biomarker screening from gene expression data by stable machine learning-recursive feature elimination methods	15
Amyloid β fibrils disruption by kolaviron: Molecular docking and extended molecular dynamics simulation studies	14
In silico prediction of peptide variants from chia (S. hispanica L.) with antimicrobial, antibiofilm, and antioxidant potential	14
Identification of epilepsy from intracranial EEG signals by using different neural network models	14
Study of the structure and binding site features of FaEXPA2, an α-expansin protein involved in strawberry fruit softening	14
N-glycosylation and ubiquitinylation of PD-L1 do not restrict interaction with BMS-202: A molecular modeling study	13
Designing of precise vaccine construct against visceral leishmaniasis through predicted epitope ensemble: A contemporary approach	13
In silico prediction of human genes as potential targets for rice miRNAs	13
C-iSUMO: A sumoylation site predictor that incorporates intrinsic characteristics of amino acid sequences	13
Clinical significance of transcription factor RUNX2 in lung adenocarcinoma and its latent transcriptional regulating mechanism	12
Molecular docking, quantum chemical computational and vibrational studies on bicyclic heterocycle “6-nitro-2,3-dihydro-1,4-benzodioxine”: Anti-cancer agent	12

Enhancing the binding of the β-sheet breaker peptide LPFFD to the amyloid-β fibrils by aromatic modifications: A molecular dynamics simulation study	12
The role of human C5a as a non-genomic target in corticosteroid therapy for management of severe COVID19	12
Genetic analysis of SARS-CoV-2 isolates collected from Bangladesh: Insights into the origin, mutational spectrum and possible pathomechanism	12
Design and various in silico studies of the novel curcumin derivatives as potential candidates against COVID-19 -associated main enzymes	12
Exploring enzyme inhibition profiles of novel halogenated chalcone derivatives on some metabolic enzymes: Synthesis, characterization and molecular modeling studies	12
Bisbenzylisoquinolines from Cissampelos pareira L. as antimalarial agents: Molecular docking, pharmacokinetics analysis, and molecular dynamic simulation studies	11
Design, synthesis, evaluation of new 3-acetylisoxazolines and their hybrid analogous as anticancer agents: In vitro and in silico analysis	11
Early diagnosis of Parkinson’s disease: A combined method using deep learning and neuro-fuzzy techniques	11
Identification of key genes of hesperidin in inhibition of breast cancer stem cells by functional network analysis	11
Ensembling machine learning models to boost molecular affinity prediction	11
A new approach for determining SARS-CoV-2 epitopes using machine learning-based in silico methods	10
Uncovering the pharmacological mechanism of motherwort (Leonurus japonicus Houtt.) for treating menstrual disorders: A systems pharmacology approach	10
Exploring two-dimensional graphene and boron-nitride as potential nanocarriers for cytarabine and clofarabine anti-cancer drugs	10
Beyond standard pipeline and p < 0.05 in pathway enrichment analyses	10
Docking-based virtual screening studies aiming at the covalent inhibition of SARS-CoV-2 MPro by targeting the cysteine 145	10
Machine learning prediction of 3CL SARS-CoV-2 docking scores	10
Mathematical modeling and analysis of the SARS-Cov-2 disease with reinfection	10
Tyrosol 1,2,3-triazole analogues as new acetylcholinesterase (AChE) inhibitors	10
Molecular simulation studies to reveal the binding mechanisms of shikonin derivatives inhibiting VEGFR-2 kinase	10
Insights into binding molecular mechanism of hemagglutinin H3N2 of influenza virus complexed with arbidol and its derivative: A molecular dynamics simulation perspective	9
Convolutional neural networks with image representation of amino acid sequences for protein function prediction	9
L2,1-Extreme Learning Machine: An Efficient Robust Classifier for Tumor Classification	9
Improved intelligent water drop-based hybrid feature selection method for microarray data processing	9
ScGSLC: An unsupervised graph similarity learning framework for single-cell RNA-seq data clustering	9
Prediction of 5-hydroxytryptamine transporter inhibitors based on machine learning	9
Computational docking investigation of phytocompounds from bergamot essential oil against Serratia marcescens protease and FabI: Alternative pharmacological strategy	9
Metaheuristics for multiple sequence alignment: A systematic review	9
Chemical characterization, computational analysis and biological views on Daphne gnidioides Jaub. & Spach extracts: Can a new raw material be provided for biopharmaceutical applications?	9
Virtual screening of dipeptidyl peptidase-4 inhibitors using quantitative structure–activity relationship-based artificial intelligence and molecular docking of hit compounds	8
Cellular and molecular level host-pathogen interactions in Francisella tularensis: A microbial gene network study	8
Experimental and theoretical studies of Palladium-hydrazide complexes’ interaction with DNA and BSA, in vitro cytotoxicity activity and plasmid cleavage ability	8
Identification of novel vaccine candidates against carbapenem resistant Klebsiella pneumoniae: A systematic reverse proteomic approach	8
The reactivity of neurotransmitters and their metabolites towards various nitrogen-centered radicals: Experimental, theoretical, and biotoxicity evaluation	8
De novo design based identification of potential HIV-1 integrase inhibitors: A pharmacoinformatics study	8
N-glycosylation of High Mobility Group Box 1 protein (HMGB1) modulates the interaction with glycyrrhizin: A molecular modeling study	8
Physicochemical properties, drug likeness, ADMET, DFT studies, and in vitro antioxidant activity of oxindole derivatives	8
Structural protein fold recognition based on secondary structure and evolutionary information using machine learning algorithms	8
A comprehensive in Silico analysis of the functional and structural impact of single nucleotide polymorphisms (SNPs) in the human IL-33 gene	8
A multilevel approach for screening natural compounds as an antiviral agent for COVID-19	8
TTRMDB: A database for structural and functional analysis on the impact of SNPs over transthyretin (TTR) using bioinformatic tools	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
Homotherapy for heteropathy active components and mechanisms of Qiang-Huo-Sheng-Shi decoction for treatment of rheumatoid arthritis and osteoarthritis	8
diSBPred: A machine learning based approach for disulfide bond prediction	8
Prognostic prediction of carcinoma by a differential-regulatory-network-embedded deep neural network	8
A representation transfer learning approach for enhanced prediction of growth hormone binding proteins	8
In-silico investigations of selective miRNA-gene targets and their validation studies in obstructive sleep apnea (OSA) patient cohorts	8
Discovery of potentially biased agonists of mu-opioid receptor (MOR) through molecular docking, pharmacophore modeling, and MD simulation	8
Lung cancer prediction using multi-gene genetic programming by selecting automatic features from amino acid sequences	8
Green synthesis of selenium based N-heterocyclic carbene compounds; structural, in-vitro anticancer and molecular docking studies	8
Exploiting reverse vaccinology approach for the design of a multiepitope subunit vaccine against the major SARS-CoV-2 variants	8
Design, semi-synthesis, anti-cancer assessment, docking, MD simulation, and DFT studies of novel theobromine-based derivatives as VEGFR-2 inhibitors and apoptosis inducers	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
In silico and in vitro studies of thiosemicarbazone-indole hybrid compounds as potent α-glycosidase inhibitors	7
ProS-GNN: Predicting effects of mutations on protein stability using graph neural networks	7
Deep_CNN_LSTM_GO: Protein function prediction from amino-acid sequences	7
Data fusion-based algorithm for predicting miRNA–Disease associations	7
Molecular dynamic simulation analysis of SARS-CoV-2 spike mutations and evaluation of ACE2 from pets and wild animals for infection risk	7
SE-BLTCNN: A channel attention adapted deep learning model based on PSSM for membrane protein classification	7
Prediction for understanding the effectiveness of antiviral peptides	7
In silico design novel (5-imidazol-2-yl-4-phenylpyrimidin-2-yl)[2-(2-pyridylamino)ethyl]amine derivatives as inhibitors for glycogen synthase kinase 3 based on 3D-QSAR, molecular docking and molecular	7
MinimapR: A parallel alignment tool for the analysis of large-scale third-generation sequencing data	7
Design and In-silico study of bioimaging fluorescence Graphene quantum dot-Bovine serum albumin complex synthesized by diimide-activated amidation	7
In silico design, synthesis and anti-HIV activity of quinoline derivatives as non-nucleoside reverse transcriptase inhibitors (NNRTIs)	7
A meta-analysis of tumor necrosis factor (TNF) gene polymorphism and susceptibility to influenza A (H1N1)	7
Effective single-cell clustering through ensemble feature selection and similarity measurements	7
In silico analysis and characterization of medicinal mushroom cystathionine beta-synthase as an angiotensin converting enzyme (ACE) inhibitory protein	7
A computational study of non-coding RNAs on the regulation of activating transcription factor 3 in human breast cancer cells	7
The Wnt pathway can stabilize hybrid phenotypes in the epithelial-mesenchymal transition: A logical modeling approach	7
Deep protein representations enable recombinant protein expression prediction	7
Modelling the spread of covid-19 in the capital of Brazil using numerical solution and cellular automata	7
Machine learning and molecular simulation ascertain antimicrobial peptide against Klebsiella pneumoniae from public database	7
Transcription factors and chaperone proteins play a role in launching a faster response to heat stress and aggregation	7
Perturbations of pathway co-expression network identify a core network in metastatic breast cancer	6
North East India medicinal plants database (NEI-MPDB)	6
LPI-CSFFR: Combining serial fusion with feature reuse for predicting LncRNA-protein interactions	6
Exploring the mechanism of Cremastra Appendiculata (SUANPANQI) against breast cancer by network pharmacology and molecular docking	6
Structure-based virtual screening of natural products as potential stearoyl-coenzyme a desaturase 1 (SCD1) inhibitors	6
FPDock: Protein–protein docking using flower pollination algorithm	6
Discovering inhibitors of TEAD palmitate binding pocket through virtual screening and molecular dynamics simulation	6
iR5hmcSC: Identifying RNA 5-hydroxymethylcytosine with multiple features based on stacking learning	6

Refined pharmacophore features for virtual screening of human thromboxane A2 receptor antagonists	6
Discovery of potential inhibitors targeting the kinase domain of polynucleotide kinase/phosphatase (PNKP): Homology modeling, virtual screening based on multiple conformations, and molecular dynamics	6
ABLE: Attention based learning for enzyme classification	6
T-A-MFFNet: Multi-feature fusion network for EEG analysis and driving fatigue detection based on time domain network and attention network	6
PmiRtarbase: A positive miRNA-target regulations database	6
ActTRANS: Functional classification in active transport proteins based on transfer learning and contextual representations	6
Transboundary Pathogenic microRNA Analysis Framework for Crop Fungi Driven by Biological Big Data and Artificial Intelligence Model	6
Polymorphic landscape of SARS-CoV-2 genomes isolated from Indian population in 2020 demonstrates rapid evolution in ORF3a, ORF8, nucleocapsid phosphoprotein and spike glycoprotein	6
Natural selection shaped the evolution of amino acid usage in mammalian toll like receptor genes	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
Identifying essential proteins using modified-monkey algorithm (MMA)	6
A tag based joint extraction model for Chinese medical text	6
Protein complex prediction in interaction network based on network motif	6
The RIT1 C-terminus associates with lipid bilayers via charge complementarity	6
Prediction of human-Streptococcus pneumoniae protein-protein interactions using logistic regression	6
Visualization of UV and ECD spectra of E&Z isomers of N-(4′-Hydroxy-cinnamoyl)− 5- hydroxyanthranilic acid	6
Clinicopathological value and underlying molecular mechanism of annexin A2 in 992 cases of thyroid carcinoma	6
Genome re-seqeunce and analysis of Burkholderia glumae strain AU6208 and evidence of toxoflavin: A potential bacterial toxin	6
QSAR-based virtual screening of traditional Chinese medicine for the identification of mitotic kinesin Eg5 inhibitors	6
Mutation-based Binary Aquila optimizer for gene selection in cancer classification	6
PALB2 as a potential prognostic biomarker for colorectal cancer	6
A network-based pharmacology study of active compounds and targets of Fritillaria thunbergii against influenza	6
Dissection of hubs and bottlenecks in a protein-protein interaction network	6
Forcefield evaluation and accelerated molecular dynamics simulation of Zn(II) binding to N-terminus of amyloid-β	6
Structure-based virtual screening of dipeptidyl peptidase 4 inhibitors and their in vitro analysis	6