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Improved prediction of protein side‐chain conformations with SCWRL4
TLDR
Accuracies as a function of electron density of the side chains demonstrate that side chains with higher electron density are easier to predict than those with low‐electron density and presumed conformational disorder. Expand
PISCES: a protein sequence culling server
TLDR
PISCES is a public server for culling sets of protein sequences from the Protein Data Bank by sequence identity and structural quality criteria and provides better lists than servers that use BLAST, which is unable to identify many relationships below 40% sequence identity. Expand
PONDR-FIT: a meta-predictor of intrinsically disordered amino acids.
TLDR
A consensus artificial neural network (ANN) prediction method, which was developed by combining the outputs of several individual disorder predictors and found to improve the prediction accuracy over a range of 3 to 20% with an average of 11% compared to the single predictors, depending on the datasets being used. Expand
A graph‐theory algorithm for rapid protein side‐chain prediction
TLDR
A new algorithm forSCWRL is presented that uses results from graph theory to solve the combinatorial problem encountered in the side‐chain prediction problem, and will allow for use of SCWRL in more demanding applications such as sequence design and ab initio structure prediction, as well addition of a more complex energy function and conformational flexibility, leading to increased accuracy. Expand
Formation of MacroH2A-containing senescence-associated heterochromatin foci and senescence driven by ASF1a and HIRA.
TLDR
Analysis of composition and mode of assembly of SAHF indicates that HIRA and ASF1a drive formation of macroH2A-containing SAHF and senescence-associated cell cycle exit, via a pathway that appears to depend on flux of heterochromatic proteins through PML bodies. Expand
Cyclic coordinate descent: A robotics algorithm for protein loop closure
TLDR
An algorithm developed originally for inverse kinematics applications in robotics, referred to as cyclic coordinate descent or CCD, involves adjusting one dihedral angle at a time to minimize the sum of the squared distances between three backbone atoms of the moving C‐terminal anchor and the corresponding atoms in the fixed C‐ terminal anchor. Expand
Bayesian statistical analysis of protein side‐chain rotamer preferences
TLDR
Bayesian statistical analysis of the conformations of side chains in proteins from the Protein Data Bank shows a strong similarity with the experimental distributions, indicating that proteins attain their lowest energy rotamers with respect to local backbone‐side‐chain interactions. Expand
Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool.
TLDR
This work presents a method for rapidly predicting the conformations of protein side-chains, starting from main-chain coordinates alone, and results compared favorably with existing methods over a comprehensive data set. Expand
Backbone-dependent rotamer library for proteins. Application to side-chain prediction.
TLDR
A backbone-dependent rotamer library for amino acid side-chains is developed and used for constructing protein side-chain conformations from the main-chain co-ordinates and it is evident from the results that a single protein does not adequately test a prediction scheme. Expand
Rotamer libraries in the 21st century.
TLDR
This work has derived well-refined rotamer libraries using strict criteria for data inclusion and for studying dependence of rotamer populations and dihedral angles on local structural features. Expand
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