Knowledge‐based protein secondary structure assignment

By Dmitrij Frishman, Patrick Argos. 1995

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Citations in the corpus

Modeling aspects of the language of life through transfer-learning protein sequences (2019, background): “The concept was quickly taken up [4 – 8] and predictions improved even more with larger families increasing evolutionary information through diversity [9, 10].”
Using AlphaFold to predict the impact of single mutations on protein stability and function (2021, background): “Information on solvent accessibility was taken from Stride [19].”
SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment (2005, methodology): “It differs from existing servers, such as WebMol (27), iMolTalk (28) and Stride ( 29 ), by providing detailed visualization and detailed contact analysis.”
Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors (2011, background): “In the structure of PCNA bound toa FEN-1 C-terminal peptide (PDB id 1RXZ [47]), the peptide consists of two parts: a b-strand (residues 1–4) connected to a short 310 helix (residues 7–11; note that the 310 helix is defined as a turn by STRIDE [48]).”
Local Protein Structures (2007, methodology): “For instance, the PB d has the geometrical feature of a β-strand, but is assigned by PSEA [241] and by STRIDE [233] to coil state with a rate equal to 19.6% and to 29.0% respectively [348].”
Estimation of the number of α‐helical and β‐strand segments in proteins using circular dichroism spectroscopy (2008, methodology): “Another algorithm of interest is STRIDE ~Frishman & Argos, 1995!, which makes use of hydrogen-bonding patterns and backbone-dihedral angles to assign thea- lix and b-sheet.”
MultiSeq: unifying sequence and structure data for evolutionary analysis (2006, methodology): “Similarly, in the structure world there are numerous tools for visualizing structural data and performing structural analyses, including RASMOL [36], STAMP [37], STRIDE [38], and 3DNA [39].”
NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy (2014, background): “S1), despite that fact that its originators have not released a new version since 2001 (Goddard and Kneller, 2008, SPARKY 3).”
The Structure, Stability and Pheromone Binding of the Male Mouse Protein Sex Pheromone Darcin (2014, methodology): “Secondary structure of darcin and MUP11 NMR structures were calculated using STRIDE webserver [39,40].”
3DRobot: automated generation of diverse and well-packed protein structure decoys (2016, background): “3DRobot protocol for protein structure decoy construction Argos, 1995), which have the hydrogen-bonding interactions in either the native or the TM-align scaffold structures.”
ProQ3: Improved model quality assessments using Rosetta energy terms (2016, methodology): “Secondary structure of the protein was calculated from the model using STRIDE [26] and predicted from the sequence using PSIPRED [27].”