ReviewPLoS computational biology2016
Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.
Review in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
What it found
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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
64 citing papers in PubMed.
- A comprehensive application of FiveFold for conformation ensemble-based protein structure prediction.Scientific reports · 2025Review
- Pioneer in Molecular Biology: Conformational Ensembles in Molecular Recognition, Allostery, and Cell Function.Journal of molecular biology · 2025Review
- A hybrid variational autoencoder and WGAN with gradient penalty for tertiary protein structure generation.Scientific reports · 2025Article
- The stability and self-assembly of tri-calcium silicate and hydroxyapatite scaffolds in bone tissue engineering applications.Journal of biological engineering · 2025Article
- Structure-based protein and small molecule generation using EGNN and diffusion models: A comprehensive review.Computational and structural biotechnology journal · 2024Review
- Host-Guest Binding Free Energies à la Carte: An Automated OneOPES Protocol.Journal of chemical theory and computation · 2024Article
- Investigation of pH-dependent Paclitaxel delivery mechanism employing Chitosan-Eudragit bioresponsive nanocarriers: a molecular dynamics simulation.Journal of biological engineering · 2024Article
- Scaffold Matcher: A CMA-ES based algorithm for identifying hotspot aligned peptidomimetic scaffolds.Proteins · 2024Article
- 3D animation as a tool for integrative modeling of dynamic molecular mechanisms.Structure (London, England : 1993) · 2024Review
- CSC01 shows promise as a potential inhibitor of the oncogenic G13D mutant of KRAS: an in silico approach.Amino acids · 2023Article
- In-silico engineering of RNA nanoplatforms to promote the diabetic wound healing.BMC chemistry · 2023Article
- Modeling of protein conformational changes with Rosetta guided by limited experimental data.Structure (London, England : 1993) · 2022Article
- Fewer Dimensions, More Structures for Improved Discrete Models of Dynamics of Free versus Antigen-Bound Antibody.Biomolecules · 2022Article
- Data Size and Quality Matter: Generating Physically-Realistic Distance Maps of Protein Tertiary Structures.Biomolecules · 2022Article
- Unraveling the Role of Charge Patterning in the Micellar Structure of Sequence-Defined Amphiphilic Peptoid Oligomers by Molecular Dynamics Simulations.Macromolecules · 2022Article
- Inverse Boltzmann Iterative Multi-Scale Molecular Dynamics Study between Carbon Nanotubes and Amino Acids.Molecules (Basel, Switzerland) · 2022Article
- Review
- AnSTAR protocols · 2021Article
- Machine Learning for Electronically Excited States of Molecules.Chemical reviews · 2021Article
- Tracking the Amide I and αCOO- Terminal ν(C=O) Raman Bands in a Family of l-Glutamic Acid-Containing Peptide Fragments: A Raman and DFT Study.Molecules (Basel, Switzerland) · 2021Article
4 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts.
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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.