ArticleJournal of computer-aided molecular design2011
Computer-aided drug design platform using PyMOL.
Article in Journal of computer-aided molecular design, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 218 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
218 citing papers in PubMed, 618 citations in OpenAlex.
- Low-frequency variants at thePharmacogenomics · 2019Trial
- Mechanistic Insights into the Antibacterial Activity of Self-Assembled Nickel(II)-Triethanolamine-Cinnamate Complexes.ACS physical chemistry Au · 2026Article
- Ginsenoside compound K inhibits migration and invasion of melanoma cells by regulating EMT via the IL-6/STAT3 signaling pathway.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Irisin maintains ER homeostasis and activates AMPK via integrin αVβ5 to attenuate CSE + LPS-induced emphysema and inflammation.Respiratory research · 2026Article
- Repeated insertions at positions 261-280 in KPC-2 highlight a ceftazidime-avibactam resistance hotspot.iScience · 2026Article
- PRMT5 promotes psoriatic inflammation through mediating dimethylation of p65 in keratinocytes.Molecular medicine (Cambridge, Mass.) · 2026Article
- Elucidation of DNA Primase as a Drug Target in Leishmania donovani: Structure-Guided Inhibitor Identification and Biochemical Validation.Chemical biology & drug design · 2026Article
- Targeting the Calcineurin Homologous Protein 1 (CHP1)-Transmembrane Protein 87A (TMEM87A) mechanosensing complex: a druggable vulnerability in metastatic ovarian cancer.Molecular biomedicine · 2026Article
- Synthesis and Characterization of Mannich-Derived 1,4-Naphthoquinones From Lawsone: Photophysical Properties, Molecular Docking, BSA/DNA Interactions, and Antioxidant Activity.Chemistry & biodiversity · 2026Article
- Exploring the mechanism of Dieda Qili Tablet on fracture healing based on network pharmacology combined with machine learning models.Scientific reports · 2026Article
- Multi-analytical and biological insights into Malcolmia grandiflora Kuntze.Scientific reports · 2026Article
- Structure-Activity Relationships, Molecular Mechanisms, and Ecotoxicological Evaluation Underlying Nucleoside-Mediated Antifouling Activity.Biomolecules · 2026Article
- Machine learning-guided composite ionic liquid-based system for dual-drug delivery targeting redox homeostasis and STAT3-PI3K axis in psoriasis therapy.Bioactive materials · 2026Article
- Multi-omics and causal inference reveal lactylation-based osteoblast regulatory networks and drug candidates.iScience · 2026Article
- Computational analysis of umami and bitter taste interactions: orthogonality in receptor-ligand binding.RSC advances · 2026Article
- Structural Model of the Oncostatin M (OSM)-OSMRβ-gp130 Ternary Complex Reveals Pathways of Allosteric Communication in OSM Signaling.Current medicinal chemistry · 2026Article
- Article
- Revealing the role of a novelFrontiers in molecular biosciences · 2026Article
- An NRIP1-Centric Monocyte Immunogenetic Bridge Between Heart Failure and Ischemic Stroke.Journal of inflammation research · 2026Article
- Structural and dynamic insights into F13L variations in monkeypox virus and their impact on tecovirimat resistance.Virology journal · 2025Article
158 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The understanding and optimization of protein-ligand interactions are instrumental to medicinal chemists investigating potential drug candidates. Over the past couple of decades, many powerful standalone tools for computer-aided drug discovery have been developed in academia providing insight into protein-ligand interactions. As programs are developed by various research groups, a consistent user-friendly graphical working environment combining computational techniques such as docking, scoring, molecular dynamics simulations, and free energy calculations is needed. Utilizing PyMOL we have developed such a graphical user interface incorporating individual academic packages designed for protein preparation (AMBER package and Reduce), molecular mechanics applications (AMBER package), and docking and scoring (AutoDock Vina and SLIDE). In addition to amassing several computational tools under one interface, the computational platform also provides a user-friendly combination of different programs. For example, utilizing a molecular dynamics (MD) simulation performed with AMBER as input for ensemble docking with AutoDock Vina. The overarching goal of this work was to provide a computational platform that facilitates medicinal chemists, many who are not experts in computational methodologies, to utilize several common computational techniques germane to drug discovery. Furthermore, our software is open source and is aimed to initiate collaborative efforts among computational researchers to combine other open source computational methods under a single, easily understandable graphical user interface.
Indexed as
Identifiers
What 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.