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Protein Structure Prediction in Drug Discovery [PDF]
Biomolecules, 2023 When the results of DeepMind’s AlphaFold2 at CASP were announced in 2020, the scientific world was so amazed by how effectively it performed that “it will change everything” became the motto for this revolution [...]
Alessandro Paiardini
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Conformational ensembles for protein structure prediction [PDF]
Scientific ReportsAcquisition of conformational ensembles for a protein is a challenging task, which is actually involving to the solution for protein folding problem and the study of intrinsically disordered protein.
Jiaan Yang +9 more
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Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms [PDF]
Genomics, Proteomics & Bioinformatics, 2023 Protein structure prediction is an interdisciplinary research topic that has attracted researchers from multiple fields, including biochemistry, medicine, physics, mathematics, and computer science.
Bin Huang +10 more
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Deep template-based protein structure prediction.
PLoS Computational Biology, 2021 MotivationProtein structure prediction has been greatly improved by deep learning, but most efforts are devoted to template-free modeling. But very few deep learning methods are developed for TBM (template-based modeling), a popular technique for protein
Fandi Wu, Jinbo Xu
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How long is a piece of loop? [PDF]
PeerJ, 2013 Loops are irregular structures which connect two secondary structure elements in proteins. They often play important roles in function, including enzyme reactions and ligand binding. Despite their importance, their structure remains difficult to predict.
Yoonjoo Choi +2 more
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TMbed: transmembrane proteins predicted through language model embeddings
BMC Bioinformatics, 2022 Background Despite the immense importance of transmembrane proteins (TMP) for molecular biology and medicine, experimental 3D structures for TMPs remain about 4–5 times underrepresented compared to non-TMPs.
Michael Bernhofer, Burkhard Rost
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Computational Approach for Protein Structure Prediction [PDF]
Healthcare Informatics Research, 2013 ObjectivesTo predict the structure of protein, which dictates the function it performs, a newly designed algorithm is developed which blends the concept of self-organization and the genetic algorithm.MethodsAmong many other approaches, genetic algorithm ...
Amouda Venkatesan +4 more
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Integrated structure-based protein interface prediction
BMC Bioinformatics, 2022 Background Identifying protein interfaces can inform how proteins interact with their binding partners, uncover the regulatory mechanisms that control biological functions and guide the development of novel therapeutic agents.
M. Walder +6 more
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DeepDist: real-value inter-residue distance prediction with deep residual convolutional network
BMC Bioinformatics, 2021 Background Driven by deep learning, inter-residue contact/distance prediction has been significantly improved and substantially enhanced ab initio protein structure prediction.
Tianqi Wu +3 more
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Non-H3 CDR template selection in antibody modeling through machine learning [PDF]
PeerJ, 2019 Antibodies are proteins generated by the adaptive immune system to recognize and counteract a plethora of pathogens through specific binding. This adaptive binding is mediated by structural diversity in the six complementary determining region (CDR ...
Xiyao Long +2 more
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