Incorporation of solvent effect into multi-objective evolutionary algorithm for improved protein structure prediction
The problem of predicting the three-dimensional (3-D) structure of a protein from its one-
dimensional sequence has been called the “holy grail of molecular biology”, and it has …
dimensional sequence has been called the “holy grail of molecular biology”, and it has …
Secondary structure and contact guided differential evolution for protein structure prediction
GJ Zhang, LF Ma, XQ Wang… - IEEE/ACM transactions on …, 2018 - ieeexplore.ieee.org
Ab initio protein tertiary structure prediction is one of the long-standing problems in structural
bioinformatics. With the help of residue-residue contact and secondary structure prediction …
bioinformatics. With the help of residue-residue contact and secondary structure prediction …
From extraction of local structures of protein energy landscapes to improved decoy selection in template-free protein structure prediction
Due to the essential role that the three-dimensional conformation of a protein plays in
regulating interactions with molecular partners, wet and dry laboratories seek biologically …
regulating interactions with molecular partners, wet and dry laboratories seek biologically …
Multi-objective stochastic search for sampling local minima in the protein energy surface
B Olson, A Shehu - Proceedings of the International Conference on …, 2013 - dl.acm.org
We present an evolutionary stochastic search algorithm to obtain a discrete representation
of the protein energy surface in terms of an ensemble of conformations representing local …
of the protein energy surface in terms of an ensemble of conformations representing local …
Generating, maintaining, and exploiting diversity in a memetic algorithm for protein structure prediction
Computational approaches to de novo protein tertiary structure prediction, including those
based on the preeminent “fragment-assembly” technique, have failed to scale up fully to …
based on the preeminent “fragment-assembly” technique, have failed to scale up fully to …
An Enhanced Genetic Algorithm for Ab Initio Protein Structure Prediction
In-vitro methods for protein structure determination are time-consuming, cost-intensive, and
failure-prone. Because of these expenses, alternative computer-based predictive methods …
failure-prone. Because of these expenses, alternative computer-based predictive methods …
Balancing multiple objectives in conformation sampling to control decoy diversity in template-free protein structure prediction
Background Computational approaches for the determination of biologically-active/native
three-dimensional structures of proteins with novel sequences have to handle several …
three-dimensional structures of proteins with novel sequences have to handle several …
Enhancing protein conformational space sampling using distance profile-guided differential evolution
GJ Zhang, XG Zhou, XF Yu, XH Hao… - IEEE/ACM transactions …, 2016 - ieeexplore.ieee.org
De novo protein structure prediction aims to search for low-energy conformations as it
follows the thermodynamics hypothesis that places native conformations at the global …
follows the thermodynamics hypothesis that places native conformations at the global …
Structure-guided protein transition modeling with a probabilistic roadmap algorithm
Proteins are macromolecules in perpetual motion, switching between structural states to
modulate their function. A detailed characterization of the precise yet complex relationship …
modulate their function. A detailed characterization of the precise yet complex relationship …
Prediction of the structures of the plant-specific regions of vascular plant cellulose synthases and correlated functional analysis
Seed plants express cellulose synthase (CESA) protein isoforms with non-redundant
functions, but how the isoforms function differently is unknown. Compared to bacterial …
functions, but how the isoforms function differently is unknown. Compared to bacterial …