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GRAMM Web Server for Protein Docking
Prediction of the structure of protein complexes by docking methods is a well-established research field. The intermolecular energy landscapes in...
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Protein–Ligand Blind Docking Using CB-Dock2
Protein–ligand blind docking is a widely used method for studying the binding sites and poses of ligands and receptors in pharmaceutical and...
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MEGADOCK-on-Colab: an easy-to-use protein–protein docking tool on Google Colaboratory
MotivationSince the advent of ColabFold, numerous software packages have been provided with Google Colaboratory-compatible ipynb files, allowing...
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A molecular docking study between heavy metals and hydrophilic Hsp70 protein to explore binding pockets
Microorganisms are abundant in whole biosphere and exert influential activities on numerous biological phenomena. The source of heavy metal...
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Ultrahigh Throughput Protein–Ligand Docking with Deep Learning
Ultrahigh-throughput virtual screening (uHTVS) is an emerging field linking together classical docking techniques with high-throughput AI methods. We...
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Unraveling the therapeutic potential of Senna singueana phytochemicals to attenuate pancreatic cancer using protein–protein interactions, molecular docking, and MD simulation
Pancreatic cancer (PC) presents challenges due to limited treatment options and patients seek complementary therapies alongside conventional...
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Spectroscopic and Molecular Docking Studies of the Interaction of Non-steroidal Anti-inflammatory Drugs with a Carrier Protein: an Interesting Case of Inner Filter Effect and Intensity Enhancement in Protein Fluorescence
Interaction of diclofenac and indomethacin with lysozyme was studied using several spectroscopic and molecular docking methods. Difference UV–visible...
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Revolutionizing drug discovery: an AI-powered transformation of molecular docking
AI-based molecular docking, a computational technique fueled by artificial intelligence (AI) algorithms, is transforming the landscape of drug...
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Mechanism of Sophorae Flavescentis Radix against ovarian cancer via new pharmacology, molecular docking, and experimental verification
The study aims to elucidate the pharmacological mechanisms of Sophorae Flavescentis Radix (SFR, Kushen) against ovarian cancer (OV) by employing an...
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Exploring the anticancer potential of fluoro flavone analogues: insights from molecular docking and dynamics studies with Aurora Kinase B
Aurora Kinase B belongs to the serine kinase family. It plays an essential role in cell division and participates in mitosis and chromatid...
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Computational modeling of PET imaging agents for vesicular acetylcholine transporter (VAChT) protein binding affinity: application of 2D-QSAR modeling and molecular docking techniques
The neurotransmitter acetylcholine (ACh) plays a ubiquitous role in cognitive functions including learning and memory with widespread innervation in...
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In-vitro antibacterial, antioxidant and anti-inflammatory and In-silico ADMET, molecular docking study on Hardwickia binata phytocompunds with potential inhibitor of skin cancer protein
The new sources of antimicrobial and antioxidant agents for methanol extracts of Hardwickia binata Roxb were evaluated systematically. The present...
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Biased Docking for Protein–Ligand Pose Prediction
The interaction between a protein and its ligands is one of the basic and most important processes in biological chemistry. Docking methods aim to...
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Molecular Docking and Computational In Silico Investigations of Metal-Based Drug Agents
The in silico computational techniques that include pharmacophores, databases, homology models, quantitative structure-activity relationships, AI...
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Unlocking therapeutic potential of trigonelline through molecular docking as a promising approach for treating diverse neurological disorders
Neurological disorders pose significant challenges in terms of treatment options, necessitating the exploration of novel therapeutic approaches....
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Epigallocatechin gallate and curcumin inhibit Bcl-2: a pharmacophore and docking based approach against cancer
The protein Bcl-2, well-known for its anti-apoptotic properties, has been implicated in cancer pathogenesis. Identifying the primary gene responsible...
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Identification of a hub gene VCL for atherosclerotic plaques and discovery of potential therapeutic targets by molecular docking
BackgroundAtherosclerosis (AS) is a pathology factor for cardiovascular diseases and instability of atherosclerotic plaques contributes to acute...
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Molecular mechanism of lycorine in the treatment of glioblastoma based on network pharmacology and molecular docking
Lycorine is a naturally active alkaloid that has been shown to have inhibitory effects on a variety of cancers. However, the underlying mechanism of...
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Identification of phytoconstituents from Dicliptera paniculata and study of antibacterial activity guided by molecular docking
According to WHO, antibiotic resistance is one of the biggest healthcare challenges to the global community. Therefore, it is absolutely essential to...
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Detailed Protocol for Predicting 3D Structure of DNA Aptamers and Performing In Silico Docking Calculations
This paper presents a comprehensive protocol for predicting the three-dimensional (3D) structure of DNA aptamers and performing in silico docking...