ReviewBriefings in bioinformatics2021
Recent advances in user-friendly computational tools to engineer protein function.
Review in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 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
24 citing papers in PubMed, 75 citations in OpenAlex.
- Computational refinement and multivalent engineering of complementarity-determining region-grafted nanobodies on a humanized scaffold for retaining antiviral efficacy.Briefings in bioinformatics · 2025Article
- InSty: A ProDy Module for Evaluating Protein Interactions and Stability.Journal of molecular biology · 2025Article
- Caver Web 2.0: analysis of tunnels and ligand transport in dynamic ensembles of proteins.Nucleic acids research · 2025Article
- Graph Neural Network-Based Approaches for Protein Function Prediction.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Systematic investigation of machine learning on limited data: A study on predicting protein-protein binding strength.Computational and structural biotechnology journal · 2024Article
- Computation-guided transcription factor biosensor specificity engineering for adipic acid detection.Computational and structural biotechnology journal · 2024Article
- Revolutionizing Molecular Design for Innovative Therapeutic Applications through Artificial Intelligence.Molecules (Basel, Switzerland) · 2024Review
- Reinforcing Tunnel Network Exploration in Proteins Using Gaussian Accelerated Molecular Dynamics.Journal of chemical information and modeling · 2024Article
- Protein engineering in the computational age: An open source framework for exploring mutational landscapesEngineering biology · 2023Article
- Mutexa: A Computational Ecosystem for Intelligent Protein Engineering.Journal of chemical theory and computation · 2023Review
- SynBioTools: a one-stop facility for searching and selecting synthetic biology tools.BMC bioinformatics · 2023Article
- Alteration of Chain-Length Selectivity and Thermostability ofApplied and environmental microbiology · 2023Article
- LibGENiE - A bioinformatic pipeline for the design of information-enriched enzyme libraries.Computational and structural biotechnology journal · 2023Article
- Transient binding sites at the surface of haloalkane dehalogenase LinB as locations for fine-tuning enzymatic activity.PloS one · 2023Article
- Enhancing the Catalytic Activity of Type II L-Asparaginase fromInternational journal of molecular sciences · 2022Article
- What Have We Learned from Design of Function in Large Proteins?Biodesign research · 2022Review
- Hardware, Software, and Wetware Codesign Environment for Synthetic Biology.Biodesign research · 2022Review
- Dawn of a New Era for Membrane Protein Design.Biodesign research · 2022Review
- Protein-Protein Interactions: Insight from Molecular Dynamics Simulations and Nanoparticle Tracking Analysis.Molecules (Basel, Switzerland) · 2021Article
- Prospects of Using Biocatalysis for the Synthesis and Modification of Polymers.Molecules (Basel, Switzerland) · 2021Review
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 at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Progress in technology and algorithms throughout the past decade has transformed the field of protein design and engineering. Computational approaches have become well-engrained in the processes of tailoring proteins for various biotechnological applications. Many tools and methods are developed and upgraded each year to satisfy the increasing demands and challenges of protein engineering. To help protein engineers and bioinformaticians navigate this emerging wave of dedicated software, we have critically evaluated recent additions to the toolbox regarding their application for semi-rational and rational protein engineering. These newly developed tools identify and prioritize hotspots and analyze the effects of mutations for a variety of properties, comprising ligand binding, protein-protein and protein-nucleic acid interactions, and electrostatic potential. We also discuss notable progress to target elusive protein dynamics and associated properties like ligand-transport processes and allosteric communication. Finally, we discuss several challenges these tools face and provide our perspectives on the further development of readily applicable methods to guide protein engineering efforts.
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.