OOIR: Observatory of International Research

Papers

(The TQCC of Journal of Computational Biophysics and Chemistry is 2. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-11-01 to 2025-11-01.)

Article	Citations
Structural Modification of Aceclofenac to Design Enhanced COX-2 Inhibitors: A Medicinal and Toxicological Study	80
The Impact of Centrality Measures in Protein–Protein Interaction Networks: Tools, Databases, Challenges and Future Directions	59
Theoretical Exploration of the Antioxidant Activity, Chemopreventive, and Antineoplastic Potentials of Molecules Present in Morinda lucida, Momordica charantia, and Vernonanthura polyanthes<	49
Virtual Screening-Based Identification of Potent DENV-3 RdRp Protease Inhibitors via In-House Usnic Acid Derivative Database	40
Poncirin Protects Against LPS-induced Acute Lung Injury: Targeting MAPKs/NF-kB Signaling Using In vivo, Molecular Docking, MD Simulation and MM-PBSA/GBSA Studies	26
GC-MS Analysis, Molecular Docking, Dynamics and ADMET Profiling of Algerian Origanum vulgare Essential Oil Compounds as Potential COVID-19 Inhibitors	24
Accurate Modeling of RNA Hairpins Through the Explicit Treatment of Electronic Polarizability with the Classical Drude Oscillator Force Field	22
Coumarin Prevents the Oligomerization and Aggregation of Amylid β: Deciphering the Mode of Action using Molecular Simulations	21
A Computational Investigation of the Glycolysis Reaction–Diffusion System via Radial Basis Function Neural Networks	21
Integrative Computational Modeling of a Multi-Epitope Vaccine to Fight Periodontal Diseases, Oral and Extra-Oral Malignancies	20
Computational Screening of Potential Fatty Acid Synthase Inhibitors as Broad-Spectrum Antiviral Agents	19
Novel Specific SARS-CoV-2 miRNAs Targeting Human Genes Involved in COVID-19 Infection and Their Regulation by Bemcentinib and Zavegepant: A Promising Evidence for RNA-Based Repurposing Therapeutic Str	19
Constructing a High-Affinity Nanobody Targeting the RSV pre-F Protein Based on AIDD and Site-Directed Mutagenesis: An Advanced In-Silico Drug Discovery Method	17
HCMdrugs: A Web-Based Database Cataloging the Drugs Available for the Treatment of Hypertrophic Cardiomyopathy	17
Molecular Docking, Molecular Dynamics Simulation, Network Pharmacology, and Therapeutic Potential of SIRT-1720 Against MPP+-induced Toxicity in SH-SY5Y Cells in Parkinson’s Disease: In Vitro Studie	16
Role of Thiophene-Based Halogenated Non-Fused Ring Containing Acceptor Molecules for Efficient Organic Photovoltaics	14
MLBKFD: Probabilistic Model Methods to Infer Pseudo Trajectories from Single-cell Data	14
Identification of Potent ABL Inhibitors from Coumestrol: An Integrative In Silico Approach	13
Utilizing Non-β-Lactam Antibiotics to Combat Antimicrobial Resistance by Targeting Multiple Virulence Factors of Pseudomonas aeruginosa	13
Pharmacokinetics, Molecular Modeling and In vitro Investigation of 4-(2-Amino-2-Carboxyethyl) Imidazole against Esophagogastric Junction Adenocarcinoma	12
Kinase Inhibitor Intervention on JIIIabc-IRES: A Novel Therapeutic Angle in HCV-Associated HCC	12
Sequence-Based Mechanistic Resolution of Amino Acid Replacement and Impact on the Activities of Peptide-Based Derivatives Targeting CXCR4 for the Treatment of Waldenström’s Macroglobulinemia	12
Application of Multi-Omics and Chemoinformatics to Analyze Oncogenic Roles and Assess Potential Inhibitors for NCAPG	11
In Silico Approaches to Reveal Structural Insights, Stability and Catalysis of Bacillus-Derived α-Amylases Prior to Advance Lab Experiments	11
Terpenoid-Based Inhibition of SQLE: Mechanistic Computational and Experimental Insights into Targeting Cholesterol Biosynthesis	10

Computational Exploration of Atriplex halimus Phytocompounds: A Targeted Approach Toward Inhibiting SARS-CoV-2	10
Leveraging Pan-Genomics, Subtractive Proteomics and Molecular Modeling to Identify Potential Drug Targets and Phytochemical Inhibitors for Leprosy Treatment	10
Computational Exploration of Berrie’s Anthocyanin as a Novel Angiotensin-Converting Enzyme Inhibitor	10
Author Index Volume 22 (2023)	10
Integrated Virtual Screening of Anthraquinone Derivatives for Anticancer Drug Discovery	10
Entropy Generation Analysis on MHD Ag+Cu/Blood Tangent Hyperbolic Hybrid Nanofluid Flow Over a Porous Plate	9
Exploring the Genetic and Molecular Connection between Autism and Huntington’s Disease via Transcriptomics and Biological Interaction Networks Analysis	9
Effect of π-Bridge in D–π–A Architecture and Adsorption of Phenothiazine Dyes on TiO2 Nanocrystalline for Dye-Sensitized Solar Cells: A DFT Approach	9
Systems Biology and Molecular Dynamics Approach for Identifying Synergistic Drug Combinations in Cancer Therapy	9
Selectivity Mechanism of Hsp90 Isoform Inhibition Through Computational Investigation	8
Electronic Structure Property and Disposal Efficiency of 2,2-Dichloropropionic Acid Using Metalloid (B, Si and Ge)-Decorated Gallium Nano-clusters (Ga₁₂X₁₂ (X = N, O))	8
Deciphering Genetic Associations: Insights into Common Molecular Pathways in Duchenne Muscular Dystrophy and Cerebral Palsy	8
Tuning of Optoelectronic Characteristics of Quinoxalineimide-based Novel Non-Fullerene Acceptors for Organic Photovoltaic Applications	8
Determining Zn(II) Binding Affinities of the YiiP–Zinc Transporter and Uno Ferro Single Chain (UFsc) Protein with a Novel Modification of the PKA17 Software	8
An Integrative Computational Approach for Design and Evaluation of Novel [1,2,4]triazolo[3,4-b][1,3,4]thiadiazole Analogues as Dual-Action Anti-Retroviral and Anti-Bacterial Agents: Insights into Rati	7
Molecular Modeling Studies to Mimic the Binding Hypothesis of NEU3 Sialidase and EGFR in Nonsmall Cell Lung Carcinoma	7
AI in PPI for Analysis of Viral Pathogens in Protein Complex Identification	7
Leveraging Subtractive Genomics to Combat Visceral Leishmaniasis: New Insights into Vaccine and Drug Target Identification	7
Selective Targeting of SARS-CoV-2 Mpro with Novel Ebsulfur-Based Compounds: A Computational Drug Discovery Approach Combining Molecular Dynamics and DFT Simulations	7
Spatially Resolved Transcriptomic Profiling of PRAME Oncogene Expression in Skin Cutaneous Melanoma: Elucidating Dermato-Oncology Therapy through Molecular Docking	7
Computational Analysis of Mutations in WNT10A Gene and Its Structural and Functional Consequences in Tooth Agenesis	7
Designing Potential Inhibitors of SARS-CoV-2 Mpro Using Deep Learning and Steered Molecular Dynamic Simulations	6
Persistent Magnitude for the Quantitative Analysis of the Structure and Stability of Carboranes	6
Exploration of Binding Interaction of β-1,3-D-Glucan and Patulin by Molecular Dynamics Simulation Study	6
Theoretical Studies on OH⁻+NH₂Cl Reaction: Nucleophilic Substitution at Neutral Nitrogen	6
Virtual Screening of PotentialIn SilicoHits for the Prevention of Neuroinflammation: Arylalkanoic Acid Derivatives of NSAIDs as Selective Dual Inhibitors of Microsomal Prostaglandin E Synthase-	6
Elucidating the Potential of Isatin Derivatives as Antimicrobial Agents: DFT Calculations and MD Simulations	6
Molybdenum Carbonyl Complexes with Benzimidazole Derivatives Against SARS-CoV-2 by Molecular Docking and DFT/TDDFT Methods	6
Newly Identified COVID-19 Drug Candidates Based on Computational Strategies	6
Transcriptomic Analysis for Elucidating the Therapeutic Potential of Sitagliptin Against the Identified TOP2A/UBE2C/CKS2 Genes as Mutually Inclusive Theragnostic Signatures of Bladder and Prostate Can	6
Synergistic Computational Techniques For Discovery of Novel Benzylidene-2,4-thiazolidinedione Derivatives as PTP1B Inhibitors	5
Elucidating DENND5A as a Therapeutic Target for Hepatocellular Carcinoma with Integrative Insights from Spatial Transcriptomics and Molecular Docking Approaches	5
Evaluation of Small Molecule Binding to the Polo-Box Domain of PLK1 at the Molecular Level	5
Discovery of Potential Natural STAT3 Inhibitors: An in silico Molecular Docking and Molecular Dynamics Study	5
Inferring Transcriptional Bursting Kinetics Using Gene Expression Model with Memory and Crosstalk from scRNA-seq Data	5
Pyrazine Linked 1,3,4-Oxadiazoles as DNA Gyrase Inhibitors: In silico Design, Molecular Docking, MM-GBSA Assay, MD Simulations and ADMET Studies	5
3D-QSAR and Molecular Docking Studies of Novel GPR52 Agonists	5
Design, Synthesis, Biological Assessment, and Computational Analysis of Sulfathiazole Schiff Bases	5
In silico High-Throughput Screening of ZINC Database of Natural Compounds to Identify Novel Histone Deacetylase Inhibitors	5
Computational Analysis and Molecular Design of Aromatic Stacking System Between Human ARTD2 Catalytic Domain and its Small-Molecule Inhibitors and Peptidic Ligands	5
Phytochemical Identification and Assessment of Amberboa ramosa Mediated Inhibition of Microtubule and EGFR Associated Growth and Metastasis of Breast Cancer Cells: In Vitro and In Sil	4
Evidence for an N-Halohistidyl Intermediate in the Catalytic Cycle of Vanadium Chloroperoxidase (VCPO) and an Artificial Enzyme Derived from VCPO: A Computational Investigation	4
Computational Insight into Electronic, Optical and Photophysical Properties of Small Compounds for Solar Cell Applications	4
Design, Synthesis, Spectroscopic Characterization, Molecular Docking and Biological Evaluation of 9H-Carbazole Linked 4-Nitrophenol: A DFT Approach	4
Pharmacophore-Based Discovery of Licoisoflavanone as a Dual CXCR4/CXCR7 Inhibitor for Coronary Artery Disease: Integration of Traditional Chinese Medicine and Modern Computational Approaches	4
Gen-AI Methods, Molecular Docking and Molecular Dynamics Simulations for Identification of Novel Inhibitors of MmPL3 Transporter of Mycobacterium tuberculosis	4
Exploring the Role of Alpinia officinarum against Acute Myeloid Leukemia using Network Pharmacology, Molecular Docking and Molecular Dynamics Simulation	4
Perfluorobiphenyl-Based Fluorescent Dyes and NLO-Phoric Systems: Unveiling Charge Transfer Dynamics and Nonlinear Optical Properties for Advanced Electro-Optic Applications	4
Virtual Screening and Molecular Docking Analysis of Degradation Products of Curcumin as Inhibitors of EGFR	4
In-vitro Isolation of Serratia marcescens and Computational Analysis of Lipase-Chitinase as a Hybrid Enzyme for the Degradation of Fungicides to Sustain the Ecosystem	4

Computational Studies of Multi-Target Directed Ligands Against Acetylcholinesterase, Butyrylcholinesterase and Amyloid Beta as Potential Anti-Alzheimer’s Agents	4
Synthesis, Characterization, Molecular Modeling Studies and Bioactivity of a Novel Bicyclic Compound of δ-lactam with Oxazepine Ring Containing Sulphur Substitute using an Economic Method	4
An Approach Towards Low Energy Loss by End-capped Modification of A2–D–A1–D–A2-type Molecules for Tuning the Photovoltaic Properties of Organic Solar Cells	4
Exploring the Optical and Photovoltaic Changeover for Carbazole-Bridge Push-Pull Switches Against Their Local Excitations and Charge Transfers	4
Application of Graph Neural Networks in Screening p38α MAPK Inhibitors in Natural Products	4
Multi-omics Data Integration via Low-Rank Representation and Data Merging for Cancer Subtypes Identification	4
Role of Near-IR Sensitive Asymmetric A–DA′D–π–A-type Non-Fullerene Acceptors for Efficient Organic Solar Cells: A Theoretical Insight	4
Synthesis, In-Silico, In Vitro and DFT Assessments of Substituted Imidazopyridine Derivatives as Potential Antimalarials Targeting Hemoglobin Degradation Pathway	4
Fine-Tuning of the Electronic and Optical Properties of Dodecabenzocoronene through Boron and Nitrogen Doping: A DFT Insight	4
Synthesis, Electronic, Dynamic Optical and Adsorption (Monte Carlo and Molecular Dynamics) Properties of Cadmium Picolinate Coordination Polymer-2 (Cp-2)	3
The Juxtaposition of Allosteric and Catalytic Inhibition in PLK1: Tradeoff for Chemotherapy and Thermodynamic Profiles of KBJK557 and BI 6727	3
In Silico Studies, Design and Synthesis of Novel Fused Pyrimidine Derivatives as a DNA Gyrase Inhibitor and Antibacterial Activity Against Quinolone Resistant Escherichia Coli	3
In Vitro Biological Screening and In Silico Molecular Modeling Studies of Thiadiazole-Bearing Benzoxazole Derivatives as Promising Acetylcholinesterase and Butyrylcholinesterase Inhibitors	3
PKAD-2: New Entries and Expansion of Functionalities of the Database of Experimentally Measured pKa’s of Proteins	3
Reactions of Hydroperoxyl Radicals (HO₂) with Oxygenated Aromatic Bio-oil Model Compounds	3
In Silico Investigation Targeting the IL-6/JAK-1/TNF-α Pathway in Rheumatoid arthritis: Matricaria chamomilla L. Compounds	3
Deep Neural Networks Predict Inhibitors ofSchistosoma MansoniThioredoxin Glutathione Reductase (SmTGR)	3
Alkali and Transition Metal-Doped 15-Crown-5 with Enhanced Nonlinear Optical Response: A DFT Study	3
Natural Products from Brazilian Biodiversity Explored as Anti-EBV Drug Candidates: In-Silico Database Mining, Docking Computations, Molecular Dynamics and DFT Calculations	3
New Antimicrobial Nitro Heteroaryl-1,3,4-Thiadiazole Derivatives Containing Piperazinyl Benzonitrile Moiety: Synthesis and in silico Study	3
Designing IL-24-P18 Fusion Protein Through Computational Engineering for Targeted Breast Cancer Therapy	3
Molecular Dynamics Studies of Mixtures of a Deep Eutectic Solvent and Cosolvents	3
Insight with Crystallization, Quantum Computation, Hirshfeld, ELF/LOL and Molecular Docking of Syringic Acid Nicotinamide Cocrystal as Potent Mycobacterium Tuberculosis Inhibitor	3
Deciphering the Selective Targeting of Noncovalent, Wild Type-sparing, and ATP-competitive Tyrosine Kinase Inhibitors to EGFR T790M Gatekeeper Mutant	3
Differentially Expressed Genes in Lung Cancer: Molecular Docking of Hypoxanthine Guanine-Phosphoribosyl Transferase with Dibutyl Phthalate	3
Advances in Molecular Modeling of Ion-Protein Interaction Systems Towards Accurate Electrostatics: Methods and Applications	3
Extensive Study of DFT-Quantum Calculations Based QSAR Modeling of Fused 1,2,4-Triazine Derivatives Revealed Potent CYP1A1 Inhibitors	3
Bioinformatics and Molecular Dynamics Studies on the Human DISC1 in Complex with the Ndel1	3
Identification of Hub Genes and Potential Drugs in Neurofibromatosis 1: An Integrated Bioinformatics Analysis	3
Structural Insights into the Interactions of Belumosudil with Rho-Associated Coiled-Coil Containing Protein Kinases 1 and 2 Based on Molecular Docking, Molecular Dynamics Simulations, and Free Energy	3
Computational Design of a Multiepitope Vaccine Targeting Rabies Virus Glycoprotein	3
Towards Development of High-Performance Perovskite Solar Cells Based on Pyrrole Materials for Hole Transport Layer by Using Computational Approach	3
In Silico Discovery of CXCR4 Inhibitors for Targeted Cancer Therapy via Pharmacophore Modeling and Molecular Simulations	2
Investigation of In-silico DFT, ADMET Prediction and Molecular Docking Insight: Synthesis and in-vitro α-Amylase Activity of Novel Benzoxazole and Benzothiazole Scaffolds	2
Spectroscopic and Theoretical Insights on Azulene-p-chloranil Charge Transfer Interaction in Solution	2
Feature Selection and Classification Technique for Predicting Lymph Node Metastasis of Papillary Thyroid Carcinoma	2
Influence of Pyramidal M20 (M= Cu, Ag and Au) Clusters on SERS and Noncovalent Interactions toward Tuberculosis Drug Pretomanid (PTD): DFT Study	2
Chitosomal Encapsulation Enhances the Anticancer Efficacy of a Theobromine Analogue: An Integrated In Silico and In Vitro Study	2
LSDDB: Lysosomal Storage Disorder Database for Lysosomal Proteins and Their Single Amino-Acid Substitutions	2
Network Pharmacology-guided Identification of Therapeutic Targets and Pathways for Cancer Stem Cell Inhibition Across Multiple Cancer Types	2
Synthesis, Structural Elucidation, Supramolecular Assembly Exploration and DFT Study of a New Ketohydrazone Derivative	2
Action Mechanism of Bioactive Compounds from Plants and Spices Mixture as Promising Anticancer Agents: In Silico Drug Design Predictions Targeting Cancer Cell Proliferation Through Cell Cycle A	2
Fragment Screening and Ligand Breeding in Designing Novel Defibrillators Preventing Alpha Synuclein Tetramer Aggregation in Parkinson’s Disease	2
In Silico Investigation of Physicochemical and Nonlinear Optical Properties of Azobenzene-Based Novel Molecules	2
In silico Design of Glyco-D,L-Peptide Antiviral Molecules	2
Machine Learning-Based Drug Repositioning of Novel Human Aromatase Inhibitors Utilizing Molecular Docking and Molecular Dynamic Simulation	2
Hydroxyethyl Urea Crystal Hydrate: Experimental and Theoretical Study	2
Entropy Generation Analysis in Blood-Gold Casson Nanofluid Through Horizontal Wavy Channel with Velocity and Thermal Slips: Applications in Skin Diseases	2
Editorial: Special Issue on Polarizable Force Fields for Biomolecular Modelling	2
Design and Discovery of Novel Quinazoline Derivatives as HER2 Inhibitors for Targeted Cancer Therapy	2
Designing a Precision Epitope-Based Vaccine Against Paragonimus westermani Using Immunoinformatics, Biophysical Analysis, and Molecular Modeling Approaches	2
Investigating the Chemical Diversity of Herg Inhibitors Using Cheminformatics and Machine Learning	2
Structural and Dynamical Properties of Carboxylate Ions in Bulk and Interfacial Water: An AIMD-MD Hybrid Study	2
Harnessing Phytochemistry to Combat Indoleamine 2,3-dioxygenase 1 and Tryptophan 2,3-dioxygenase 2 in Restoring Tryptophan Homeostasis in Ovarian Cancer	2
Structural Insights and Drug Repurposing of FDA-Approved Molecules against Human Agmatinase in Cancer Therapy	2
Extensive In-silico Target-Ligand Conformational Space Sampling of Garlic-Derived Sulfur Compounds Targeting COVID-19 Infection	2
Engineering and Molecular Dynamics Simulation of DNA Origami–Heparin Nanostructures for Antiviral Applications	2
Microemulsion of Medicago marina Essential Oil: In Vitro Evaluation of Antimicrobial, Antibiofilm, Anticoagulant Effects, and In Silico Studies Involving Molecular Docking and ADM	2
Neighborhood Path Complex for the Quantitative Analysis of the Structure and Stability of Carboranes	2
New Drug Analogues as Aromatase Inhibitors: A Perspective from High-Throughput Docking and Molecular Dynamics Simulations	2
An In Silico Analysis Integrating Bulk and Single-Cells RNA Sequencing to Study the Mechanistic Effects of Umbelliferone in COPD	2
Exploring Key Proteins, Pathways and Oxygen Usage Bias of Proteins and Metabolites in Melanoma	2
MembIT – A Tool to Calculate Solute Membrane Insertions and Deformations in Molecular Dynamics Simulations	2
Achieving The Molecular Structural Identity and Functional Characterization of Newly Imidazole Derivative: Elucidation of Quantum Computational Approach and Topological Investigation	2
Synthesis, Characterization, Density Functional Theory, Monte Carlo, and Molecular Dynamics Simulations of [Ni(Ii)(Tpy)₂] Metal Organic Framework and Congo Red Dye Application	2
Dual Therapeutic Potential of Novel Cornallegic Acid: In Vitro Anti-inflammatory and ROS Suppression with Computational Insights from Docking, ADMET and DFT Studies	2
Author Index Volume 21 (2022)	2
A comparative study of the size-modified and classical Poisson-Boltzmann models with sharp and diffuse interfaces	2
Schiff Bases from α-ionone with Adenine, Cytosine, and l-leucine Biomolecules: Synthesis, Structural Features, Electronic Structure, and Medicinal Activities	2
DFT Study for Adsorbing of Bromine Monochloride onto BNNT (5,5), BNNT (7,0), BC₂NNT (5,5), and BC₂NNT (7,0)	2
Investigating the Role of Novel Benzotrithiophene-Based Bat-Shaped Non-Fullerene Acceptors for High Performance Organic Solar Cells	2
Influence of Iodine Merz–Singh–Kollman Radius on the Calculated Charges and Hydration Free Energies of Iodinated Molecules	2
Symmetry Breaking and Charge Delocalization as Key Drivers Toward Tuning Electronic, Static and Frequency-Dependent NLO Properties in Alkali Metal-Substituted [Mn; M =Li, Na, K; n =1–4] Tetracyclopent	2
Testing and Optimizing the Drude Polarizable Force Field for Blocked Amino Acids Based on High-Level Quantum-Mechanical Energy Surfaces	2
Pharmacophore-Based Virtual Screening Toward the Discovery of Novel GLUT1 Inhibitors	2
Novel Cholesterol-Based Dihydropyrimidinone Derivatives with Potential Biological Activities: An In-silico Investigation	2
Targeting Pathogenic Desulfovibrio Species with a Novel Multi-Epitope Vaccine: A Reverse Vaccinology and Computational Approach	2
Erratum: Designing Potential Inhibitors of SARS-CoV-2 Mpro Using Deep Learning and Steered Molecular Dynamic Simulations	2
Investigating Chlorpromazine’s Role in Attenuating Quorum Sensing and Biofilm in Gram-negative Bacteria	2
A Multi-target Study of Natural Compounds in Preventing Neurodegenerative Disease Progression: A Computational Modeling Study	2