ReviewJournal of molecular modeling2025
A comprehensive review on structural insights through molecular visualization: tools, applications, and limitations.
Review in Journal of molecular modeling, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
4 citing papers in PubMed.
- Beyond the flat screen: evaluating virtual reality as a complementary tool for molecular docking in drug discovery.Journal of computer-aided molecular design · 2026Review
- AI-driven fungicide design: From target identification to field application.Plant communications · 2026Review
- Strategic Computational Design of siRNA Molecules Targeting Structural Genes of SARS-CoV-2.Applied biochemistry and biotechnology · 2026Article
- Artificial Intelligence in Cardiovascular Health: Insights into Post-COVID Public Health Challenges.High blood pressure & cardiovascular prevention : the official journal of the Italian Society of Hypertension · 2025Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
contextBiomolecules serve as intrinsic repositories of information related to function, binding interactions, molecular motion, and structural conformations. With the rapid accumulation of structural data from fields such as structural biology and cheminformatics, the ability to visualize biomolecular architecture has become essential for researchers in biology, pharmacology, and related disciplines. Molecular visualization represents a foundational step in accessing and interpreting this data, enabling its application in diverse scientific and therapeutic contexts. Recent advancements in computational algorithms and web-based visualization platforms have provided powerful resources for structural biologists, chemists, and crystallographers, facilitating efficient analysis and reproducibility of experimental outcomes. This review offers a comprehensive overview of contemporary molecular visualization tools, emphasizing their practical applications. Particular attention is given to PyMOL and NGL Viewer, with detailed guidance for their implementation in visualizing proteins, DNA, protein-ligand complexes, protein-protein interactions, protein-DNA assemblies, and small molecule ligands. Challenges frequently encountered in structural biology and cheminformatics, such as the identification of lead compounds for therapeutic development, are also addressed. Molecular dynamics simulations, including binding free energy calculations, are discussed as cost- and time-effective strategies to enhance drug discovery pipelines. In response to the increasing complexity of data-driven research, this review aims to serve as a valuable resource for professionals seeking efficient, reliable visualization tools to support structure-based research and drug design.
methodsThis review article provides a comprehensive comparative analysis of biomolecular visualization features integrated into standalone and web-based molecular visualization tools. PyMOL (standalone) and NGL (web-based) were systematically employed to visualize proteins, ligands, protein-ligand complexes, protein-protein complexes, and protein-DNA complexes. The methodological framework outlined in this study establishes standardized guidelines for the effective utilization of molecular visualization tools, offering valuable insights for structural biologists and researchers engaged in molecular modeling and structural analysis.
Indexed as
Identifiers
40423839What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.