Mapping the Protein Universe

By Liisa Holm, Christopher Sander. 1996

Subfields: Computational Biology & Bioinformatics

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Citations in the corpus

Learning protein sequence embeddings using information from structure (2019, methodology): “However, these methods are only appropriate for matching proteins with high sequence similarity [2, 3, 30].”
Protein 3D Structure Computed from Evolutionary Sequence Variation (2011, background): “. Additional interesting potential applications include (2) a survey of the arrangements of trans-membrane segments in membrane proteins; (3) discovery of remote evolutionary homologies by comparison of 3D structures beyond the power of sequence profiles”
Protein sectors: evolutionary units of three-dimensional structure (2009, background): “This description derives from the basic chemical properties of polypeptide chains and empirical observation, and is the basis for current classifications and comparative analyses of protein families (Holm and Sander, 1996; Orengo and Thornton, 2005; Thornton et al., 1999).”
Practical limits of function prediction (2000, background): “5), considered to provide more reliable structural alignments.(23)”
An overview of the structures of protein-DNA complexes (2000, unknown): “A2(103-160), B1(5-75), B2(102-161) 1oct C1(5-75) Oct-1 POU domain H.”
The structure of the protein universe and genome evolution (2002, background): “In particular, the discovery of the uniformly distributed background microwave radiation is the main proof of the Big Bang model of the Universe's origin (for example, see ref”
Dali server update (2016, methodology): “The Dali program optimizes a structural alignment, that is, a sequential set of one-to-one correspondences between C-alpha atoms (13,14).”
CATHEDRAL: A Fast and Effective Algorithm to Predict Folds and Domain Boundaries from Multidomain Protein Structures (2007, methodology): “Furthermore, certain motifs, described as ‘‘ attractors, ’’ occur as the core of a protein’s structure more frequently than others [36].”
Improvement of the GenTHREADER Method for Genomic Fold Recognition (2003, methodology): “A set of 2727 FSSP files were downloaded from the FSSP database (Holm and Sander, 1996) at ftp://ftp.ebi.ac.uk in the directory /pub/databases/fssp. (N.B.”
The evolving role of natural products in drug discovery (2005, background): “These units are combined in modular fashion to fine-tune the function of full protein”