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   Articles with "predicting protein" as a keyword



Predicting protein stability and solubility changes upon mutations: data perspective

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recommendations! Published in 2020 at "ChemCatChem"

DOI: 10.1002/cctc.202000933

Abstract: Understanding mutational effects on protein stability and solubility is of particular importance for creating industrially relevant biocatalysts, resolving mechanisms of many human diseases, and producing efficient biopharmaceuticals, to name a few. For in silico predictions,… read more here.

Keywords: predicting protein; protein stability; stability solubility; solubility changes ... See more keywords
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An insightful recollection for predicting protein subcellular locations in multi-label systems.

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recommendations! Published in 2019 at "Genomics"

DOI: 10.1016/j.ygeno.2019.08.008

Abstract: A systematic introduction has been presented for the recent advances in predicting protein subcellular localization in the multi-label systems, where the constituent proteins may simultaneously occur or move between two or more location sites and… read more here.

Keywords: predicting protein; recollection predicting; multi label; label systems ... See more keywords

Predicting Protein Function in the AI and Big Data Era

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recommendations! Published in 2025 at "Biochemistry"

DOI: 10.1021/acs.biochem.5c00186

Abstract: It is an exciting time for researchers working to link proteins to their functions. Most techniques for extracting functional information from genomic sequences were developed several years ago, with major progress driven by the availability… read more here.

Keywords: protein function; predicting protein; data era; function big ... See more keywords

Predicting Protein-Peptide Complex Structures by Accounting for Peptide Flexibility and the Physicochemical Environment

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recommendations! Published in 2022 at "Journal of chemical information and modeling"

DOI: 10.1021/acs.jcim.1c00836

Abstract: Predicting protein-peptide complex structures is crucial to the understanding of a vast variety of peptide-mediated cellular processes and to peptide-based drug development. Peptide flexibility and binding mode ranking are the two major challenges for protein-peptide… read more here.

Keywords: peptide; protein peptide; predicting protein; peptide complex ... See more keywords

Predicting Protein-Ligand Binding and Unbinding Kinetics with Biased MD Simulations and Coarse-Graining of Dynamics: Current State and Challenges

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recommendations! Published in 2023 at "Journal of chemical information and modeling"

DOI: 10.1021/acs.jcim.3c00151

Abstract: The prediction of drug-target binding and unbinding kinetics that occur on time scales between milliseconds and several hours is a prime challenge for biased molecular dynamics simulation approaches. This Perspective gives a concise summary of… read more here.

Keywords: predicting protein; binding unbinding; unbinding kinetics; current state ... See more keywords

Predicting Protein-Peptide Interactions: Benchmarking Deep Learning Techniques and a Comparison with Focused Docking.

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recommendations! Published in 2023 at "Journal of chemical information and modeling"

DOI: 10.1021/acs.jcim.3c00602

Abstract: The accurate prediction of protein structures achieved by deep learning (DL) methods is a significant milestone and has deeply impacted structural biology. Shortly after its release, AlphaFold2 has been evaluated for predicting protein-peptide interactions and… read more here.

Keywords: interactions benchmarking; predicting protein; protein peptide; peptide interactions ... See more keywords
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A Machine Learning Protocol for Predicting Protein Infrared Spectra.

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recommendations! Published in 2020 at "Journal of the American Chemical Society"

DOI: 10.1021/jacs.0c06530

Abstract: Infrared (IR) absorption provides important chemical fingerprints of biomolecules. Protein secondary structure determination from IR spectra is tedious since its theoretical interpretation requires repeated expensive quantum-mechanical calculations in a fluctuating environment. Herein we present a… read more here.

Keywords: protein; machine learning; predicting protein; protocol predicting ... See more keywords

Biomimetic fusion: Platyper's dual vision for predicting protein-surface interactions.

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recommendations! Published in 2024 at "Materials horizons"

DOI: 10.1039/d4mh00066h

Abstract: Predicting protein binding with the material surface still remains a challenge. Here, a novel approach, platypus dual perception neural network (Platyper), was developed to describe the interactions in protein-surface systems involving bioceramics with BMPs. The… read more here.

Keywords: surface interactions; predicting protein; dual vision; protein surface ... See more keywords

Predicting protein–membrane interfaces of peripheral membrane proteins using ensemble machine learning

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recommendations! Published in 2022 at "Briefings in Bioinformatics"

DOI: 10.1093/bib/bbab518

Abstract: Abstract Abnormal protein–membrane attachment is involved in deregulated cellular pathways and in disease. Therefore, the possibility to modulate protein–membrane interactions represents a new promising therapeutic strategy for peripheral membrane proteins that have been considered so… read more here.

Keywords: peripheral membrane; predicting protein; membrane proteins; machine learning ... See more keywords

NetSolP: predicting protein solubility in Escherichia coli using language models

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recommendations! Published in 2022 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btab801

Abstract: MOTIVATION Solubility and expression levels of proteins can be a limiting factor for large-scale studies and industrial production. By determining the solubility and expression directly from the protein sequence, the success rate of wet-lab experiments… read more here.

Keywords: language models; escherichia coli; netsolp predicting; predicting protein ... See more keywords

Predicting protein stability changes upon mutation using a simple orientational potential

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recommendations! Published in 2023 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btad011

Abstract: Abstract Motivation Structure-based stability prediction upon mutation is crucial for protein engineering and design, and for understanding genetic diseases or drug resistance events. For this task, we adopted a simple residue-based orientational potential that considers… read more here.

Keywords: predicting protein; upon mutation; stability; orientational potential ... See more keywords