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Protein Structure Prediction Using Rosetta
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions.
- K. Simons, C. Kooperberg, E. Huang, D. Baker
- Computer ScienceJournal of Molecular Biology
- 25 April 1997
The effects of multiple sequence information and different types of conformational constraints on the overall performance of the method are investigated, and the ability of a variety of recently developed scoring functions to recognize the native-like conformations in the ensembles of simulated structures are investigated.
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.
Protein structure prediction and analysis using the Robetta server
The Robetta server provides automated tools for protein structure prediction and analysis and current capabilities include the prediction of the effects of mutations on protein-protein interactions using computational interface alanine scanning.
Improving physical realism, stereochemistry, and side‐chain accuracy in homology modeling: Four approaches that performed well in CASP8
Four approaches that address the “last mile of the protein folding problem” and have performed well during CASP8, yielding physically realistic models are described.
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.
Contact order, transition state placement and the refolding rates of single domain proteins.
Investigations have revealed statistically significant correlations between the average sequence separation between contacting residues in the native state and the rate and transition state placement of folding for a non-homologous set of simple, single domain proteins, indicating that proteins featuring primarily sequence-local contacts tend to fold more rapidly and exhibit less compact folding transition states than those characterized by more non-local interactions.
Toward High-Resolution de Novo Structure Prediction for Small Proteins
The prediction of protein structure from amino acid sequence is a grand challenge of computational molecular biology and the primary bottleneck to consistent high-resolution prediction appears to be conformational sampling.
A simple physical model for binding energy hot spots in protein–protein complexes
The results test the understanding of the dominant contributions to the free energy of protein–protein interactions, can guide experiments aimed at the design of protein interaction inhibitors, and provide a stepping-stone to important applications such as interface redesign.
Improved protein structure prediction using predicted interresidue orientations
- Jianyi Yang, I. Anishchenko, Hahnbeom Park, Zhenling Peng, S. Ovchinnikov, D. Baker
- BiologyProceedings of the National Academy of Sciences
- 18 November 2019
A deep residual network for predicting interresidue orientations, in addition to distances, and a Rosetta-constrained energy-minimization protocol for rapidly and accurately generating structure models guided by these restraints are developed.