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- Publications
- Influence
Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction
The distance‐dependent structure‐derived potentials developed so far all employed a reference state that can be characterized as a residue (atom)‐averaged state. Here, we establish a new reference… Expand
Protein binding site prediction using an empirical scoring function
Most biological processes are mediated by interactions between proteins and their interacting partners including proteins, nucleic acids and small molecules. This work establishes a method called… Expand
SPINE-D: Accurate Prediction of Short and Long Disordered Regions by a Single Neural-Network Based Method
- Tuo Zhang, E. Faraggi, B. Xue, A. Dunker, V. Uversky, Y. Zhou
- Mathematics, Medicine
- Journal of biomolecular structure & dynamics
- 1 February 2012
Abstract Short and long disordered regions of proteins have different preference for different amino acid residues. Different methods often have to be trained to predict them separately. In this… Expand
SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures
- Hongyi Zhou, Y. Zhou
- Computer Science, Medicine
- Bioinform.
- 15 September 2005
TLDR
Fold recognition by combining sequence profiles derived from evolution and from depth‐dependent structural alignment of fragments
Recognizing structural similarity without significant sequence identity has proved to be a challenging task. Sequence‐based and structure‐based methods as well as their combinations have been… Expand
Capturing non‐local interactions by long short‐term memory bidirectional recurrent neural networks for improving prediction of protein secondary structure, backbone angles, contact numbers and…
- Rhys Heffernan, Yuedong Yang, K. Paliwal, Y. Zhou
- Physics, Computer Science
- Bioinform.
- 15 September 2017
TLDR
Single‐body residue‐level knowledge‐based energy score combined with sequence‐profile and secondary structure information for fold recognition
An elaborate knowledge‐based energy function is designed for fold recognition. It is a residue‐level single‐body potential so that highly efficient dynamic programming method can be used for… Expand
Achieving 80% ten‐fold cross‐validated accuracy for secondary structure prediction by large‐scale training
TLDR
Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden‐Markov‐model‐based method
- H. Zhou, Y. Zhou
- Computer Science, Medicine
- Protein science : a publication of the Protein…
- 1 July 2003
TLDR
Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native…
- Yuedong Yang, E. Faraggi, Huiying Zhao, Y. Zhou
- Computer Science, Medicine
- Bioinform.
- 1 August 2011
TLDR