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	100
Geo-Measures: A PyMOL plugin for protein structure ensembles analysis	81
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	78
Synthesis, structural elucidation, DFT calculation, biological studies and DNA interaction of some aryl hydrazone Cr3+, Fe3+, and Cu2+ chelates	66
Tuning hyperparameters of machine learning algorithms and deep neural networks using metaheuristics: A bioinformatics study on biomedical and biological cases	66
Predicting potential miRNA-disease associations by combining gradient boosting decision tree with logistic regression	65
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	60
Incorporating deep learning and multi-omics autoencoding for analysis of lung adenocarcinoma prognostication	57
Repurposing approved drugs as potential inhibitors of 3CL-protease of SARS-CoV-2: Virtual screening and structure based drug design	54
A deep learning approach based on convolutional LSTM for detecting diabetes	53
Exploring the mechanism of action Xianlingubao Prescription in the treatment of osteoporosis by network pharmacology	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
Design, molecular docking analysis of an anti-inflammatory drug, computational analysis and intermolecular interactions energy studies of 1-benzothiophene-2-carboxylic acid	48
BERT-Promoter: An improved sequence-based predictor of DNA promoter using BERT pre-trained model and SHAP feature selection	48
A Recurrent Neural Network model to predict blood–brain barrier permeability	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
SETE: Sequence-based Ensemble learning approach for TCR Epitope binding prediction	40
Inferring LncRNA-disease associations based on graph autoencoder matrix completion	40
Structure-based virtual screening of influenza virus RNA polymerase inhibitors from natural compounds: Molecular dynamics simulation and MM-GBSA calculation	39
Computational study of 3-thiophene acetic acid: Molecular docking, electronic and intermolecular interactions investigations	37
Exploration of the mechanism of Zisheng Shenqi decoction against gout arthritis using network pharmacology	32
In silico modeling for dual inhibition of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) enzymes in Alzheimer’s disease	32
Protein kinase inhibitors’ classification using K-Nearest neighbor algorithm	32
Network pharmacology analysis of Chaihu Lizhong Tang treating non-alcoholic fatty liver disease	31

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
Intelligent system based on data mining techniques for prediction of preterm birth for women with cervical cerclage	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
A global report on the dynamics of COVID-19 with quarantine and hospitalization: A fractional order model with non-local kernel	28
Efficient machine learning model for predicting drug-target interactions with case study for Covid-19	27
Designing a potent L1 protein-based HPV peptide vaccine: A bioinformatics approach	27
Atom counting method for determining elemental composition of viruses and its applications in biothermodynamics and environmental science	26
Theoretical analysis of bacterial efflux pumps inhibitors: Strategies in-search of competent molecules and develop next	26
ncRDeep: Non-coding RNA classification with convolutional neural network	25
Genome-wide analysis of the MADS-Box gene family in Chrysanthemum	25
An in-silico approach to study the possible interactions of miRNA between human and SARS-CoV2	25
LMI-DForest: A deep forest model towards the prediction of lncRNA-miRNA interactions	24
Designing, characterization, biological, DFT, and molecular docking analysis for new FeAZD, NiAZD, and CuAZD complexes incorporating 1-(2-hydroxyphenylazo)− 2-naphthol (H2AZD)	23
Computational prediction of protein ubiquitination sites mapping on Arabidopsis thaliana	23
Cholinesterases, carbonic anhydrase inhibitory properties and in silico studies of novel substituted benzylamines derived from dihydrochalcones	23
Apache Spark based kernelized fuzzy clustering framework for single nucleotide polymorphism sequence analysis	22
Predicting novel CircRNA-disease associations based on random walk and logistic regression model	22
A machine learning approach to select features important to stroke prognosis	22
Alkylated benzimidazoles: Design, synthesis, docking, DFT analysis, ADMET property, molecular dynamics and activity against HIV and YFV	22
Swarm intelligence based clustering technique for automated lesion detection and diagnosis of psoriasis	22
lncRNA-miRNA-mRNA interaction network for colorectal cancer; An in silico 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
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
Comprehensive analyses of bioinformatics applications in the fight against COVID-19 pandemic	20
CWLy-SVM: A support vector machine-based tool for identifying cell wall lytic enzymes	18
GanDTI: A multi-task neural network for drug-target interaction prediction	17
RNA-Seq analysis reveals pluripotency-associated genes and their interaction networks in human embryonic stem cells	17
Exploring of antioxidant and antibacterial properties of novel 1,3,4-thiadiazole derivatives: Facile synthesis, structural elucidation and DFT approach to antioxidant characteristics	17
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	16
iPiDA-sHN: Identification of Piwi-interacting RNA-disease associations by selecting high quality negative samples	16
Profiling the structural determinants of pyrrolidine derivative as gelatinases (MMP-2 and MMP-9) inhibitors using in silico approaches	16
DeepAdd: Protein function prediction from k-mer embedding and additional features	16
MD-UNET: Multi-input dilated U-shape neural network for segmentation of bladder cancer	16
Dual computational and biological assessment of some promising nucleoside analogs against the COVID-19-Omicron variant	15
Identification of potential inhibitors of human methionine aminopeptidase (type II) for cancer therapy: Structure-based virtual screening, ADMET prediction and molecular dynamics studies	15
A DFT study on the metal ion selectivity of deferiprone complexes	15
A review of Cloud computing technologies for comprehensive microRNA analyses	15
The severity prediction of the binary and multi-class cardiovascular disease − A machine learning-based fusion approach	15
Bioinformatics analysis and verification of gene targets for renal clear cell carcinoma	15
In silico prediction of peptide variants from chia (S. hispanica L.) with antimicrobial, antibiofilm, and antioxidant potential	14
Robust biomarker screening from gene expression data by stable machine learning-recursive feature elimination methods	14
In silico and in vitro assessment of androgen receptor antagonists	14
Virtual screening using docking and molecular dynamics of cannabinoid analogs against CB1 and CB2 receptors	14
Study of the structure and binding site features of FaEXPA2, an α-expansin protein involved in strawberry fruit softening	14
Amyloid β fibrils disruption by kolaviron: Molecular docking and extended molecular dynamics simulation studies	14
Identification of epilepsy from intracranial EEG signals by using different neural network models	14
In silico prediction of human genes as potential targets for rice miRNAs	13

TAP 1.0: A robust immunoinformatic tool for the prediction of tumor T-cell antigens based on AAindex properties	13
Computational modeling of imines based anti-oxidant and anti-esterases compounds: Synthesis, single crystal and In-vitro assessment	13
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
Clinical significance of transcription factor RUNX2 in lung adenocarcinoma and its latent transcriptional regulating mechanism	12
C-iSUMO: A sumoylation site predictor that incorporates intrinsic characteristics of amino acid sequences	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
Molecular docking, quantum chemical computational and vibrational studies on bicyclic heterocycle “6-nitro-2,3-dihydro-1,4-benzodioxine”: Anti-cancer agent	12
Genetic analysis of SARS-CoV-2 isolates collected from Bangladesh: Insights into the origin, mutational spectrum and possible pathomechanism	12
Structure-based discovery of novel inhibitors of Mycobacterium tuberculosis CYP121 from Indonesian natural products	11
Early diagnosis of Parkinson’s disease: A combined method using deep learning and neuro-fuzzy techniques	11
In-silico analysis of cucumber (Cucumis sativus L.) Genome for WRKY transcription factors and cis-acting elements	11
Ensembling machine learning models to boost molecular affinity prediction	11
Design and various in silico studies of the novel curcumin derivatives as potential candidates against COVID-19 -associated main enzymes	11
The role of human C5a as a non-genomic target in corticosteroid therapy for management of severe COVID19	11
Design, synthesis, evaluation of new 3-acetylisoxazolines and their hybrid analogous as anticancer agents: In vitro and in silico analysis	11
Identification of key genes of hesperidin in inhibition of breast cancer stem cells by functional network analysis	11
A new approach for determining SARS-CoV-2 epitopes using machine learning-based in silico methods	10
Machine learning prediction of 3CL SARS-CoV-2 docking scores	10
Exploring enzyme inhibition profiles of novel halogenated chalcone derivatives on some metabolic enzymes: Synthesis, characterization and molecular modeling studies	10
Mathematical modeling and analysis of the SARS-Cov-2 disease with reinfection	10
Exploring two-dimensional graphene and boron-nitride as potential nanocarriers for cytarabine and clofarabine anti-cancer drugs	10
Tyrosol 1,2,3-triazole analogues as new acetylcholinesterase (AChE) inhibitors	10
Docking-based virtual screening studies aiming at the covalent inhibition of SARS-CoV-2 MPro by targeting the cysteine 145	10
Beyond standard pipeline and p < 0.05 in pathway enrichment analyses	10
Identification of key genes and expression profiles in osteoarthritis by co-expressed network analysis	10
Protein structure optimization using improved simulated annealing algorithm on a three-dimensional AB off-lattice model	10
Convolutional neural networks with image representation of amino acid sequences for protein function prediction	9
Uncovering the pharmacological mechanism of motherwort (Leonurus japonicus Houtt.) for treating menstrual disorders: A systems pharmacology approach	9
Prediction of 5-hydroxytryptamine transporter inhibitors based on machine learning	9
Insights into binding molecular mechanism of hemagglutinin H3N2 of influenza virus complexed with arbidol and its derivative: A molecular dynamics simulation perspective	9
Bisbenzylisoquinolines from Cissampelos pareira L. as antimalarial agents: Molecular docking, pharmacokinetics analysis, and molecular dynamic simulation studies	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
Molecular simulation studies to reveal the binding mechanisms of shikonin derivatives inhibiting VEGFR-2 kinase	9
ScGSLC: An unsupervised graph similarity learning framework for single-cell RNA-seq data clustering	9
L2,1-Extreme Learning Machine: An Efficient Robust Classifier for Tumor Classification	9
A representation transfer learning approach for enhanced prediction of growth hormone binding proteins	8
Cellular and molecular level host-pathogen interactions in Francisella tularensis: A microbial gene network study	8
The reactivity of neurotransmitters and their metabolites towards various nitrogen-centered radicals: Experimental, theoretical, and biotoxicity evaluation	8
TTRMDB: A database for structural and functional analysis on the impact of SNPs over transthyretin (TTR) using bioinformatic tools	8
diSBPred: A machine learning based approach for disulfide bond prediction	8
De novo design based identification of potential HIV-1 integrase inhibitors: A pharmacoinformatics study	8
Prognostic prediction of carcinoma by a differential-regulatory-network-embedded deep neural network	8
Physicochemical properties, drug likeness, ADMET, DFT studies, and in vitro antioxidant activity of oxindole derivatives	8
Design of (quinolin-4-ylthio)carboxylic acids as new Escherichia coli DNA gyrase B inhibitors: machine learning studies, molecular docking, synthesis and biological testing	8
Structure-based modeling of turnover of Bcl-2 family proteins bound to voltage-dependent anion channel 2 (VDAC2): Implications for the mechanisms of proapoptotic activation of Bak and Bax in vivo	8
Identification of novel vaccine candidates against carbapenem resistant Klebsiella pneumoniae: A systematic reverse proteomic approach	8
Computational docking investigation of phytocompounds from bergamot essential oil against Serratia marcescens protease and FabI: Alternative pharmacological strategy	8
Identifying critical states of hepatocellular carcinoma based on landscape dynamic network biomarkers	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
Metaheuristics for multiple sequence alignment: A systematic review	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
Experimental and theoretical studies of Palladium-hydrazide complexes’ interaction with DNA and BSA, in vitro cytotoxicity activity and plasmid cleavage ability	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
conLSH: Context based Locality Sensitive Hashing for mapping of noisy SMRT reads	8
Improved intelligent water drop-based hybrid feature selection method for microarray data processing	8
N-glycosylation of High Mobility Group Box 1 protein (HMGB1) modulates the interaction with glycyrrhizin: A molecular modeling study	8
Virtual screening of dipeptidyl peptidase-4 inhibitors using quantitative structure–activity relationship-based artificial intelligence and molecular docking of hit compounds	8
The Wnt pathway can stabilize hybrid phenotypes in the epithelial-mesenchymal transition: A logical modeling approach	7
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	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
A meta-analysis of tumor necrosis factor (TNF) gene polymorphism and susceptibility to influenza A (H1N1)	7
Transcription factors and chaperone proteins play a role in launching a faster response to heat stress and aggregation	7
Discovery of potentially biased agonists of mu-opioid receptor (MOR) through molecular docking, pharmacophore modeling, and MD simulation	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
Homotherapy for heteropathy active components and mechanisms of Qiang-Huo-Sheng-Shi decoction for treatment of rheumatoid arthritis and osteoarthritis	7
In silico identification of potential inhibitors against human 2’-5’- oligoadenylate synthetase (OAS) proteins	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
Lung cancer prediction using multi-gene genetic programming by selecting automatic features from amino acid sequences	7
A multilevel approach for screening natural compounds as an antiviral agent for COVID-19	7
A computational study of non-coding RNAs on the regulation of activating transcription factor 3 in human breast cancer cells	7
Exploiting reverse vaccinology approach for the design of a multiepitope subunit vaccine against the major SARS-CoV-2 variants	7
Deep_CNN_LSTM_GO: Protein function prediction from amino-acid sequences	7
Design and In-silico study of bioimaging fluorescence Graphene quantum dot-Bovine serum albumin complex synthesized by diimide-activated amidation	7
In-silico investigations of selective miRNA-gene targets and their validation studies in obstructive sleep apnea (OSA) patient cohorts	7
Triple Mycobacterial ATP-synthase mutations impedes Bedaquiline binding: Atomistic and structural perspectives	7
Effective single-cell clustering through ensemble feature selection and similarity measurements	7

Green synthesis of selenium based N-heterocyclic carbene compounds; structural, in-vitro anticancer and molecular docking studies	7
In silico and in vitro studies of thiosemicarbazone-indole hybrid compounds as potent α-glycosidase inhibitors	7
Insights regarding novel biomarkers and the pathogenesis of primary colorectal carcinoma based on bioinformatic analysis	6
Transboundary Pathogenic microRNA Analysis Framework for Crop Fungi Driven by Biological Big Data and Artificial Intelligence Model	6
ProS-GNN: Predicting effects of mutations on protein stability using graph neural networks	6
LPI-CSFFR: Combining serial fusion with feature reuse for predicting LncRNA-protein interactions	6
Mutation-based Binary Aquila optimizer for gene selection in cancer classification	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
Refined pharmacophore features for virtual screening of human thromboxane A2 receptor antagonists	6
The RIT1 C-terminus associates with lipid bilayers via charge complementarity	6
ABLE: Attention based learning for enzyme classification	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
ActTRANS: Functional classification in active transport proteins based on transfer learning and contextual representations	6
Exploring the mechanism of Cremastra Appendiculata (SUANPANQI) against breast cancer by network pharmacology and molecular docking	6
Molecular insight for the role of key residues of calreticulin in its binding activities: A computational study	6
Genome re-seqeunce and analysis of Burkholderia glumae strain AU6208 and evidence of toxoflavin: A potential bacterial toxin	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
Protein complex prediction in interaction network based on network motif	6
Perturbations of pathway co-expression network identify a core network in metastatic breast cancer	6
Structure-based virtual screening of dipeptidyl peptidase 4 inhibitors and their in vitro analysis	6
North East India medicinal plants database (NEI-MPDB)	6
Clinicopathological value and underlying molecular mechanism of annexin A2 in 992 cases of thyroid carcinoma	6
MinimapR: A parallel alignment tool for the analysis of large-scale third-generation sequencing data	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
QSAR-based virtual screening of traditional Chinese medicine for the identification of mitotic kinesin Eg5 inhibitors	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
In silico design, synthesis and anti-HIV activity of quinoline derivatives as non-nucleoside reverse transcriptase inhibitors (NNRTIs)	6
Forcefield evaluation and accelerated molecular dynamics simulation of Zn(II) binding to N-terminus of amyloid-β	6
SE-BLTCNN: A channel attention adapted deep learning model based on PSSM for membrane protein classification	6
Machine learning and molecular simulation ascertain antimicrobial peptide against Klebsiella pneumoniae from public database	6
In silico analysis and characterization of medicinal mushroom cystathionine beta-synthase as an angiotensin converting enzyme (ACE) inhibitory protein	6