ArticleProtein science : a publication of the Protein Society2021
The Bio3D packages for structural bioinformatics.
Article in Protein science : a publication of the Protein Society, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 247 papers.
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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.
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Who cites it
247 citing papers in PubMed.
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- Ligand-mediated conformation diversity of Hsp90 revealed by GaMD simulations and Markov model.Molecular diversity · 2026Article
- C620Y Mutation-Induced Destabilization of the Androgen Receptor Disrupts DNA Recognition Specificity in Prostate Cancer: Insights from Extensive Parametric Normal Mode Simulations.Cell biochemistry and biophysics · 2026Article
- Computational insights and activity evaluation of novel SHP-2 inhibitors for targeting type 2 diabetes mellitus.Molecular diversity · 2026Article
- Molecular determinants of TNFR1:TNFα binding and dynamics in a physiological membrane environment.Current research in structural biology · 2026Article
- Quantum chemical optimization and residue-specific stabilization of CDK20 inhibitors in hepatocellular carcinoma.Molecular diversity · 2026Article
- MDNA : a software module for DNA structure generation and analysis.Nucleic acids research · 2026Article
- Oligomeric assemblies of plant biotin carboxylase revealed by cryo-EM and cross-linking.The Biochemical journal · 2026Article
- The structural basis of RanGAP1 regulation and catalysis in nuclear transport.bioRxiv : the preprint server for biology · 2026Article
- Hidden structural states of proteins revealed by conformer selection.Nature communications · 2026Article
187 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
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bio3D is a family of R packages for the analysis of biomolecular sequence, structure, and dynamics. Major functionality includes biomolecular database searching and retrieval, sequence and structure conservation analysis, ensemble normal mode analysis, protein structure and correlation network analysis, principal component, and related multivariate analysis methods. Here, we review recent package developments, including a new underlying segregation into separate packages for distinct analysis, and introduce a new method for structure analysis named ensemble difference distance matrix analysis (eDDM). The eDDM approach calculates and compares atomic distance matrices across large sets of homologous atomic structures to help identify the residue wise determinants underlying specific functional processes. An eDDM workflow is detailed along with an example application to a large protein family. As a new member of the Bio3D family, the Bio3D-eddm package supports both experimental and theoretical simulation-generated structures, is integrated with other methods for dissecting sequence-structure-function relationships, and can be used in a highly automated and reproducible manner. Bio3D is distributed as an integrated set of platform independent open source R packages available from: http://thegrantlab.org/bio3d/.
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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.