A graph‐theory algorithm for rapid protein side‐chain prediction

By Adrian A. Canutescu, Andrew A. Shelenkov, Roland L. Dunbrack. Protein Science, 2003

1,085 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a59b5da1de93e35bbb26d335ca2247ea710a9315

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In Materials Chemistry

In Molecular Biology

Citations in the corpus

I-TASSER server for protein 3D structure prediction (2008, neutral): “0 [27] to build side-chain rotamers.”
Refinement of unreliable local regions in template‐based protein models (2012, methodology): “After loop closure, side chains of the loop residues are re-modeled using an in-house version of SCWRL. 36 A 0.2-ps MD simulation is then carried out on ULR at fixed protein framework.”
GalaxyRefine: protein structure refinement driven by side-chain repacking (2013, background): “The physics-based energy function contains CHARMM22-based molecular-mechanics bonded energy terms (22), Lennard–Jones interaction energy, Coulomb potential energy, FACTS solvation free energy (23) and solvent accessible surface area energy, whereas the database-derived energy function contains hydro”
Linear Programming Relaxations and Belief Propagation - An Empirical Study (2006, methodology): “Using the SCWRL energy function (Canutescu et al., 2003), which approximates the repulsive portion of Lennard-Jones 12-6 potential.”
Software for molecular docking: a review (2017, background): “The CLIX program attempts to make a pair of favorable interactions in the binding site of the protein with a pair of chemical substitutions (Lawrence and Davis 1992).”
Prediction of amino acid side chain conformation using a deep neural network (2017, methodology): “Of the prediction methods currently available, Side Chain With Rotamer Library 4 (SCWRL4)(6, 12) is the most widelyused method because it is accurate and fast.”
AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed ab initio models. (2012, methodology): “In order to take advantage of the specialized side-chain addition tool SCWRL (Canutescu et al., 2003; Krivov et al., 2009), with its backbone-dependent rotamer libraries, the side chains that were added during the rapidrelax procedure of Rosetta were remodelled using SCWRL.”
Principles of Flexible Protein-Protein Docking (2008, background): “100,101 A proposed bound function is defined for a certain level, and yields a lower bound of energy, obtainable from any branch below this level.”