machine-learning protein structure prediction program alphafold2 Search Results


machine learning algorithm alphafold2  (Deepmind Technologies Ltd)
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Deepmind Technologies Ltd machine learning algorithm alphafold2
Molecular characterisation of HCO_011565 and docking with UMW-868. (A) Structure of HCO_011565 protein predicted in silico using the <t>Alphafold2</t> algorithm. The per-residue confidence scores (pLDDT; left to right) for individual sections of the protein are indicated. (B) Transcription and expression profiles for the gene encoding HCO_011565 in different developmental stages/sexes of Haemonchus contortus larvae: eggs, first-, second- and third-stage larvae (L1, L2 and L3, respectively), exsheathed third-stage larvae (xL3s), fourth-stage larvae (L4s), female and male L4s (L4f and L4m, respectively), and female and male adults (Af and Am, respectively). Heatmaps indicate levels of transcription/expression: red indicates moderate to high transcription/expression; green is low expression; and grey indicates that expression was not detected. (C) Three-dimensional structure of the protein HCO_011565 and its interaction with compound UMW-868; the inset shows the positioning of UMW-868 in the pocket predicted within HCO_011565. (D) Phylogenetic relationship of protein HCO_011565 with its orthologs in five other species of nematode (left) and the structural models of these orthologs predicted using Alphafold (right).
Machine Learning Algorithm Alphafold2, supplied by Deepmind Technologies Ltd, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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alphafold2  (Deepmind Technologies Ltd)
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Deepmind Technologies Ltd alphafold2
Molecular characterisation of HCO_011565 and docking with UMW-868. (A) Structure of HCO_011565 protein predicted in silico using the <t>Alphafold2</t> algorithm. The per-residue confidence scores (pLDDT; left to right) for individual sections of the protein are indicated. (B) Transcription and expression profiles for the gene encoding HCO_011565 in different developmental stages/sexes of Haemonchus contortus larvae: eggs, first-, second- and third-stage larvae (L1, L2 and L3, respectively), exsheathed third-stage larvae (xL3s), fourth-stage larvae (L4s), female and male L4s (L4f and L4m, respectively), and female and male adults (Af and Am, respectively). Heatmaps indicate levels of transcription/expression: red indicates moderate to high transcription/expression; green is low expression; and grey indicates that expression was not detected. (C) Three-dimensional structure of the protein HCO_011565 and its interaction with compound UMW-868; the inset shows the positioning of UMW-868 in the pocket predicted within HCO_011565. (D) Phylogenetic relationship of protein HCO_011565 with its orthologs in five other species of nematode (left) and the structural models of these orthologs predicted using Alphafold (right).
Alphafold2, supplied by Deepmind Technologies Ltd, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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december 2020  (Deepmind Technologies Ltd)
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Deepmind Technologies Ltd december 2020
Molecular characterisation of HCO_011565 and docking with UMW-868. (A) Structure of HCO_011565 protein predicted in silico using the <t>Alphafold2</t> algorithm. The per-residue confidence scores (pLDDT; left to right) for individual sections of the protein are indicated. (B) Transcription and expression profiles for the gene encoding HCO_011565 in different developmental stages/sexes of Haemonchus contortus larvae: eggs, first-, second- and third-stage larvae (L1, L2 and L3, respectively), exsheathed third-stage larvae (xL3s), fourth-stage larvae (L4s), female and male L4s (L4f and L4m, respectively), and female and male adults (Af and Am, respectively). Heatmaps indicate levels of transcription/expression: red indicates moderate to high transcription/expression; green is low expression; and grey indicates that expression was not detected. (C) Three-dimensional structure of the protein HCO_011565 and its interaction with compound UMW-868; the inset shows the positioning of UMW-868 in the pocket predicted within HCO_011565. (D) Phylogenetic relationship of protein HCO_011565 with its orthologs in five other species of nematode (left) and the structural models of these orthologs predicted using Alphafold (right).
December 2020, supplied by Deepmind Technologies Ltd, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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autodock vina  (AUTODOCK GmbH)
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AUTODOCK GmbH autodock vina
Molecular characterisation of HCO_011565 and docking with UMW-868. (A) Structure of HCO_011565 protein predicted in silico using the <t>Alphafold2</t> algorithm. The per-residue confidence scores (pLDDT; left to right) for individual sections of the protein are indicated. (B) Transcription and expression profiles for the gene encoding HCO_011565 in different developmental stages/sexes of Haemonchus contortus larvae: eggs, first-, second- and third-stage larvae (L1, L2 and L3, respectively), exsheathed third-stage larvae (xL3s), fourth-stage larvae (L4s), female and male L4s (L4f and L4m, respectively), and female and male adults (Af and Am, respectively). Heatmaps indicate levels of transcription/expression: red indicates moderate to high transcription/expression; green is low expression; and grey indicates that expression was not detected. (C) Three-dimensional structure of the protein HCO_011565 and its interaction with compound UMW-868; the inset shows the positioning of UMW-868 in the pocket predicted within HCO_011565. (D) Phylogenetic relationship of protein HCO_011565 with its orthologs in five other species of nematode (left) and the structural models of these orthologs predicted using Alphafold (right).
Autodock Vina, supplied by AUTODOCK GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


Molecular characterisation of HCO_011565 and docking with UMW-868. (A) Structure of HCO_011565 protein predicted in silico using the Alphafold2 algorithm. The per-residue confidence scores (pLDDT; left to right) for individual sections of the protein are indicated. (B) Transcription and expression profiles for the gene encoding HCO_011565 in different developmental stages/sexes of Haemonchus contortus larvae: eggs, first-, second- and third-stage larvae (L1, L2 and L3, respectively), exsheathed third-stage larvae (xL3s), fourth-stage larvae (L4s), female and male L4s (L4f and L4m, respectively), and female and male adults (Af and Am, respectively). Heatmaps indicate levels of transcription/expression: red indicates moderate to high transcription/expression; green is low expression; and grey indicates that expression was not detected. (C) Three-dimensional structure of the protein HCO_011565 and its interaction with compound UMW-868; the inset shows the positioning of UMW-868 in the pocket predicted within HCO_011565. (D) Phylogenetic relationship of protein HCO_011565 with its orthologs in five other species of nematode (left) and the structural models of these orthologs predicted using Alphafold (right).

Journal: Frontiers in Pharmacology

Article Title: Thermal proteome profiling reveals Haemonchus orphan protein HCO_011565 as a target of the nematocidal small molecule UMW-868

doi: 10.3389/fphar.2022.1014804

Figure Lengend Snippet: Molecular characterisation of HCO_011565 and docking with UMW-868. (A) Structure of HCO_011565 protein predicted in silico using the Alphafold2 algorithm. The per-residue confidence scores (pLDDT; left to right) for individual sections of the protein are indicated. (B) Transcription and expression profiles for the gene encoding HCO_011565 in different developmental stages/sexes of Haemonchus contortus larvae: eggs, first-, second- and third-stage larvae (L1, L2 and L3, respectively), exsheathed third-stage larvae (xL3s), fourth-stage larvae (L4s), female and male L4s (L4f and L4m, respectively), and female and male adults (Af and Am, respectively). Heatmaps indicate levels of transcription/expression: red indicates moderate to high transcription/expression; green is low expression; and grey indicates that expression was not detected. (C) Three-dimensional structure of the protein HCO_011565 and its interaction with compound UMW-868; the inset shows the positioning of UMW-868 in the pocket predicted within HCO_011565. (D) Phylogenetic relationship of protein HCO_011565 with its orthologs in five other species of nematode (left) and the structural models of these orthologs predicted using Alphafold (right).

Article Snippet: The three-dimensional structures of proteins were predicted using the machine learning algorithm AlphaFold2 , which is an advanced, artificial intelligence (AI) program—developed by DeepMind and acquired by Alphabet/Google; this program uses a neural network (deep-learning) ( ) to predict the three-dimensional structures of proteins from their primary amino acid sequences, and achieves high levels of accuracy/confidence compared with conventional, homology-based modelling methods.

Techniques: In Silico, Residue, Expressing