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Abstract The recent breakthroughs in structure prediction, where methods such as AlphaFold demonstrated near‐atomic accuracy, herald a paradigm shift in structural biology. The 200 million high‐accuracy models released in the AlphaFold Database are expected to guide protein science in the coming decades. Partitioning these AlphaFold models into domains and assigning them to an evolutionary hierarchy provide an efficient way to gain functional insights into proteins. However, classifying such a large number of predicted structures challenges the infrastructure of current structure classifications, including our Evolutionary Classification of protein Domains (ECOD). Better computational tools are urgently needed to parse and classify domains from AlphaFold models automatically. Here we present a Domain Parser for AlphaFold Models (DPAM) that can automatically recognize globular domains from these models based on inter‐residue distances in 3D structures, predicted aligned errors, and ECOD domains found by sequence (HHsuite) and structural (Dali) similarity searches. Based on a benchmark of 18,759 AlphaFold models, we demonstrate that DPAM can recognize 98.8% of domains and assign correct boundaries for 87.5%, significantly outperforming structure‐based domain parsers and homology‐based domain assignment using ECOD domains found by HHsuite or Dali. Application of DPAM to the massive AlphaFold models will enable efficient classification of domains, providing evolutionary contexts and facilitating functional studies.
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Wallace : A flexible platform for reproducible modeling of species niches and distributions built for community expansion
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The femora of diapsids have undergone morphological changes related to shifts in postural and locomotor modes, such as the transition from plesiomorphic amniote and diapsid taxa to the apomorphic conditions related to a more erect posture within Archosauriformes. One remarkable clade of Triassic diapsids is the chameleon-like Drepanosauromorpha. This group is known from numerous articulated but heavily compressed skeletons that have the potential to further inform early reptile femoral evolution. For the first time, we describe the three-dimensional osteology of the femora of Drepanosauromorpha, based on undistorted fossils from the Upper Triassic Chinle Formation and Dockum Group of North America. We identify apomorphies and a combination of character states that link these femora to those in crushed specimens of drepanosauromorphs and compare our sample with a range of amniote taxa. Several characteristics of drepanosauromorph femora, including a hemispherical proximal articular surface, prominent asymmetry in the proximodistal length of the tibial condyles, and a deep intercondylar sulcus, are plesiomorphies shared with early diapsids. The femora contrast with those of most diapsids in lacking a crest-like, distally tapering internal trochanter. They bear a ventrolaterally positioned tuberosity on the femoral shaft, resembling the fourth trochanter in Archosauriformes. The reduction of an internal trochanter parallels independent reductions in therapsids and archosauriforms. The presence of a ventrolaterally positioned trochanter is also similar to that of chameleonid squamates. Collectively, these features demonstrate a unique femoral morphology for drepanosauromorphs, and suggest an increased capacity for femoral adduction and protraction relative to most other Permo-Triassic diapsids.more » « less
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Accepted Manuscript
- Journal Article:
- https://doi.org/10.1111/2041-210X.12945
