Improved recognition of native‐like protein structures using a combination of sequence‐dependent and sequence‐independent features of proteins

By K. Simons, Ingo Ruczinski, Charles L. Kooperberg, B. A. Fox, C. Bystroff, David Baker. 1999

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Citations in the corpus

Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement (2013, methodology): “Rosetta’s protocol to predict protein structures from their sequence alone runs in two phases: a low-resolution phase (ab initio) relying on fragment insertion (Simons, Kooperberg, Huang, & Baker, 1997) to search through a relatively smooth energy landscape (Simons et al., 1999), and a high-resoluti”
The Rosetta all-atom energy function for macromolecular modeling and design (2017, background): “33 These terms were for low-resolution modeling, meaning that the scores were dependent on only the coordinates of the backbone atoms and that interactions between the side chains were treated implicitly.”
Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information (2014, methodology): “…side-chains are represented by fixed center-of-mass atoms allowing for rapid generation and evaluation of various protein-like topologies; the second stage (‘full-atom’) builds in explicit side-chains and carries out all atom energy minimization ( Simons et al., 1999 ; Raman et al., 2009 ).”
Large-scale determination of previously unsolved protein structures using evolutionary information (2015, methodology): “…structures of proteins from large families with no representatives of known structure by integrating co-evolution derived contact information from GREMLIN ( Kamisetty et al., 2013 ) into the Rosetta structure prediction methodology ( Simons et al., 1999 ; Rohl et al., 2004 ; Raman et al., 2009 ).”
A position-specific distance-dependent statistical potential for protein structure and functional study (2012, background): “…1996, 1997), decoy ranking (Bauer and Beyer, 1994; Casari and Sippl, 1992; Gatchell et al., 2000; Hendlich et al., 1990; Samudrala and Moult, 1998; Simons et al., 1999; Vendruscolo et al., 2000), and protein model quality assessment (Jones and Thornton, 1996; Panchenko et al., 2000; Peng and Xu,…”
SCRATCH: a protein structure and structural feature prediction server (2005, methodology): “Two terms in the energy function are based directly on statistics from the PDB, one for residue environments (11,12) and another for bond angles.”
High-resolution Structural and Thermodynamic Analysis of Extreme Stabilization of Human Procarboxypeptidase by Computational Protein Design (2007, background): “The energy function is a linear combination of a 6-12 Lennard-Jones potential, the Lazaridis – Karplus implicit solvation model, 47 an empirical hydrogen bonding potential, 48 backbone-dependent rotamer probabilities, 49 amino acid probabilities for particular regions of ϕ / ψ space, and a simple el”
Modeling structurally variable regions in homologous proteins with rosetta (2004, methodology): “We describe a method based on the successful de novo structure prediction method Rosetta 3,4 for modeling SVRs.”
Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers (2011, methodology): “The protein internal energy is calculated using Rosetta’s standard lowresolution potential function, which has terms capturing van der Waals interactions, residue environment and residue-pair preferences, and backbone torsion strain (45).”
De novo protein structure determination using sparse NMR data (2000, methodology): “To ameliorate regions where our estimation of theφψ was either ambiguous or mistaken, we augmented the library with fragments chosen by agreement with the multiple sequence alignment and the sequence-based predicted secondary structure (Simons et al., 1997, 1999b).”
Statistical potentials for fold assessment (2002, unknown): “…and Jernigan 1996, 2000; Reva et al 1997; Jones 1999b; Kolinski et al. 1999; Panchenko et al. 2000; Skolnick et al. 2000), detection of native-like protein conformations (Hendlich et al. 1990; Casari and Sippl 1992; Bauer and Beyer 1994; Samudrala and Moult 1998; Simons et al. 1999; Gatchell et”