Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation

By S. Miyazawa, Robert L. Jernigan. 1985

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Citations in the corpus

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model (2016, methodology): “, position-specific scoring matrix), predicted 3-state secondary structure and 3-state solvent accessibility, direct co-evolutionary information generated by CCMpred, mutual information and pairwise potential (Betancourt and Thirumalai, 1999; Miyazawa and Jernigan, 1985).”
Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement (2013, methodology): “…energy—has been used to justify creating knowledge-based potentials from distribution of features from crystal structures (Miyazawa & Jernigan, 1985; Sippl, 1990); for example, rotamer libraries are often based on feature distributions (Dunbrack & Karplus, 1993; Ponder…”
MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins (2014, methodology): “The mean contact potential is computed by averaging contact potential terms (Betancourt and Thirumalai, 1999; Miyazawa and Jernigan, 1985) across the two alignment columns.”
Folding membrane proteins by deep transfer learning (2017, methodology): “The pairwise features include co-evolution strength generated by CCMpred (Seemayer et al., 2014), mutual information and pairwise contact potential (Miyazawa and Jernigan, 1985, Betancourt and Thirumalai, 1999).”
A position-specific distance-dependent statistical potential for protein structure and functional study (2012, background): “Previous studies (Bradley et al., 2005; Skolnick, 2006) indicate that knowledge-based statistical potentials (Lu et al., 2008; Miyazawa and Jernigan, 1985; Shen and Sali, 2006; Simons et al., 1997; Sippl, 1990; Tanaka and Scheraga, 1976; Zhang and Zhang, 2010; Zhou and Zhou, 2002) compare favorably…”
New statistical potential for quality assessment of protein models and a survey of energy functions (2010, background): “The residue level representations use C a , C b atoms or side chain centroids and are usually based on the 20 naturally occurring amino acids [2,15,24,25], although both reduced [7,26,27] and extended [28,29] amino acid alphabets were explored, where the extended alphabet further classifies each…”
The MARTINI Coarse-Grained Force Field: Extension to Proteins. (2008, background): “Bonded Interactions. Bonded interactions are described by the following set of potential energy functions acting between bonded sites i, j, k, and l with equilibrium distance db, angle φa, and dihedral angles ψd and ψid: Vb ) 1 2 Kb(dij -db) 2 ( 3 )”
Principles of docking: An overview of search algorithms and a guide to scoring functions (2002, methodology): “(cid:12) G ACE is the atomic contact energy ( ACE ), an extension of the quasi-chemical residue pair-wise potential (Miyazawa and Jernigan 253 ).”
Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details. (2009, background): “…analyses of the forces between atoms (Brooks et al., 1983; Pearlman et al., 1995; Lazaridis and Karplus, 2000), and knowledge-based potentials (KBP), which rely on statistical analysis of different properties extracted from protein databases (Tanaka and Scheraga, 1976; Miyazawa and Jernigan, 1985).”