alphafold2 software (Deepmind Technologies Ltd)

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Deepmind Technologies Ltd alphafold2 software

Figure 1. Schematic illustration of our ligand-search protocol and examples of identiﬁed metal binding sites in <t>AlphaFold2</t> structures. (a) a ﬂowchart outlining the method. For the protein illustrated in the center of the ﬂowchart, two “regions” are highlighted; these are distinct from one another, and are treated as separate entities when enumerating all possible ligand superpositions. (b) an example of an identiﬁed 4Fe-4S cluster coordinated by four cysteine residues (ligand type “4Fe-4S Cys4”; UniProt accession: P08201). (c) an example of a cluster of three closely spaced Zn binding sites coordinated by a total of eight cysteine residues; this cluster is formed by three successful additions of the ligand type “Zn Cys4” (UniProt accession: P05100). In all images of proteins in this ﬁgure, the protein is colored by each residue’s pLDDT score with dark blue indicating a “very high conﬁdence” prediction by AlphaFold2 and dark red indicting a “low conﬁdence” prediction.

Alphafold2 Software, 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
https://www.bioz.com/product/program+alphafold2/pm34838520-0-1-0?v=Deepmind+Technologies+Ltd
Average 86 stars, based on 1 article reviews

alphafold2 software - by Bioz Stars, 2026-08

86/100 stars

Images

1) Product Images from "Identification of Iron-Sulfur (Fe-S) Cluster and Zinc (Zn) Binding Sites Within Proteomes Predicted by DeepMind's AlphaFold2 Program Dramatically Expands the Metalloproteome."

Article Title: Identification of Iron-Sulfur (Fe-S) Cluster and Zinc (Zn) Binding Sites Within Proteomes Predicted by DeepMind's AlphaFold2 Program Dramatically Expands the Metalloproteome.

Journal: Journal of molecular biology

doi: 10.1016/j.jmb.2021.167377

Figure 1. Schematic illustration of our ligand-search protocol and examples of identiﬁed metal binding sites in AlphaFold2 structures. (a) a ﬂowchart outlining the method. For the protein illustrated in the center of the ﬂowchart, two “regions” are highlighted; these are distinct from one another, and are treated as separate entities when enumerating all possible ligand superpositions. (b) an example of an identiﬁed 4Fe-4S cluster coordinated by four cysteine residues (ligand type “4Fe-4S Cys4”; UniProt accession: P08201). (c) an example of a cluster of three closely spaced Zn binding sites coordinated by a total of eight cysteine residues; this cluster is formed by three successful additions of the ligand type “Zn Cys4” (UniProt accession: P05100). In all images of proteins in this ﬁgure, the protein is colored by each residue’s pLDDT score with dark blue indicating a “very high conﬁdence” prediction by AlphaFold2 and dark red indicting a “low conﬁdence” prediction.

Figure Legend Snippet: Figure 1. Schematic illustration of our ligand-search protocol and examples of identiﬁed metal binding sites in AlphaFold2 structures. (a) a ﬂowchart outlining the method. For the protein illustrated in the center of the ﬂowchart, two “regions” are highlighted; these are distinct from one another, and are treated as separate entities when enumerating all possible ligand superpositions. (b) an example of an identiﬁed 4Fe-4S cluster coordinated by four cysteine residues (ligand type “4Fe-4S Cys4”; UniProt accession: P08201). (c) an example of a cluster of three closely spaced Zn binding sites coordinated by a total of eight cysteine residues; this cluster is formed by three successful additions of the ligand type “Zn Cys4” (UniProt accession: P05100). In all images of proteins in this ﬁgure, the protein is colored by each residue’s pLDDT score with dark blue indicating a “very high conﬁdence” prediction by AlphaFold2 and dark red indicting a “low conﬁdence” prediction.

Techniques Used: Binding Assay

Figure 6. Example 4Fe-4S cluster binding sites annotated in UniProt that are not identiﬁed in this work. In each image protein chains are shown as transparent cartoons colored using AlphaFold20s pLDDT (i.e. conﬁdence) scores on a spectrum of red (low conﬁdence) to blue (high conﬁdence), coordinating residues are shown as licorice, and iron and sulfur atoms in the 4Fe-4S cluster are shown as yellow and pink spheres, respectively. (a) an example in which AlphaFold2 builds two 4Fe-4S sites out of residues annotated in two different UniProt sites but swaps two cysteine residues between each of the sites: the two UniProt sites are shown with their carbon atoms colored in either cyan or green and the residue numbers for the corresponding sites are displayed above the image with arrows to indicate the cysteines that are swapped. (b) an example in which AlphaFold2 conﬁdently builds a “4Fe-4S Cys4” site as “4Fe-4S Cys3” site and rejects the annotation of the fourth residue. (c) an example in which AlphaFold2 does not build the UniProt-annotated residues into a 4Fe-4S binding site but instead conﬁdently builds the residues in an a helix (opaque blue cartoon).

Figure Legend Snippet: Figure 6. Example 4Fe-4S cluster binding sites annotated in UniProt that are not identiﬁed in this work. In each image protein chains are shown as transparent cartoons colored using AlphaFold20s pLDDT (i.e. conﬁdence) scores on a spectrum of red (low conﬁdence) to blue (high conﬁdence), coordinating residues are shown as licorice, and iron and sulfur atoms in the 4Fe-4S cluster are shown as yellow and pink spheres, respectively. (a) an example in which AlphaFold2 builds two 4Fe-4S sites out of residues annotated in two different UniProt sites but swaps two cysteine residues between each of the sites: the two UniProt sites are shown with their carbon atoms colored in either cyan or green and the residue numbers for the corresponding sites are displayed above the image with arrows to indicate the cysteines that are swapped. (b) an example in which AlphaFold2 conﬁdently builds a “4Fe-4S Cys4” site as “4Fe-4S Cys3” site and rejects the annotation of the fourth residue. (c) an example in which AlphaFold2 does not build the UniProt-annotated residues into a 4Fe-4S binding site but instead conﬁdently builds the residues in an a helix (opaque blue cartoon).

Techniques Used: Binding Assay, Residue

Figure 7. Example 2Fe-2S cluster binding sites annotated in UniProt that are not identiﬁed in this work; visualization scheme is the same as used in Figure 6. (a) An example in which AlphaFold2 conﬁdently builds disulﬁde bonds in the annotated UniProt site. (b) An example in which AlphaFold2 conﬁdently builds a potential site that is too constricted to coordinate a 2Fe-2S cluster. (c) An example in which AlphaFold2 builds the fourth coordinating residue in a position that is more than 5 A from the three other coordinating residues. (d) An example in which AlphaFold2 builds a potential 2Fe-2S site with a different fourth coordinating residue (carbon atom colored green) than that which is annotated in UniProt (red arrow).

Figure Legend Snippet: Figure 7. Example 2Fe-2S cluster binding sites annotated in UniProt that are not identiﬁed in this work; visualization scheme is the same as used in Figure 6. (a) An example in which AlphaFold2 conﬁdently builds disulﬁde bonds in the annotated UniProt site. (b) An example in which AlphaFold2 conﬁdently builds a potential site that is too constricted to coordinate a 2Fe-2S cluster. (c) An example in which AlphaFold2 builds the fourth coordinating residue in a position that is more than 5 A from the three other coordinating residues. (d) An example in which AlphaFold2 builds a potential 2Fe-2S site with a different fourth coordinating residue (carbon atom colored green) than that which is annotated in UniProt (red arrow).

Techniques Used: Binding Assay, Residue

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alphafold2 software (Deepmind Technologies Ltd)

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Images

1) Product Images from "Identification of Iron-Sulfur (Fe-S) Cluster and Zinc (Zn) Binding Sites Within Proteomes Predicted by DeepMind's AlphaFold2 Program Dramatically Expands the Metalloproteome."

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