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Prediction of protein stability changes for single-site mutations using support vector machines.
Accurate prediction of protein stability changes resulting from single amino acid mutations is important for understanding protein structures and designing new proteins. We use support vector… Expand
SCRATCH: a protein structure and structural feature prediction server
- J. Cheng, A. Randall, Michael J. Sweredoski, P. Baldi
- Computer Science, Medicine
- Nucleic Acids Res.
- 27 June 2005
SCRATCH is a server for predicting protein tertiary structure and structural features. The SCRATCH software suite includes predictors for secondary structure, relative solvent accessibility,… Expand
A large-scale evaluation of computational protein function prediction
Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If… Expand
Improved residue contact prediction using support vector machines and a large feature set
BackgroundPredicting protein residue-residue contacts is an important 2D prediction task. It is useful for ab initio structure prediction and understanding protein folding. In spite of steady… Expand
Three-stage prediction of protein ?-sheets by neural networks, alignments and graph algorithms
MOTIVATION Protein beta-sheets play a fundamental role in protein structure, function, evolution and bioengineering. Accurate prediction and assembly of protein beta-sheets, however, remains… Expand
Accurate Prediction of Protein Disordered Regions by Mining Protein Structure Data
- J. Cheng, Michael J. Sweredoski, P. Baldi
- Computer Science
- Data Mining and Knowledge Discovery
- 1 November 2005
Intrinsically disordered regions in proteins are relatively frequent and important for our understanding of molecular recognition and assembly, and protein structure and function. From an algorithmic… Expand
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
- Yuxiang Jiang, Tal Ronnen Oron, +144 authors P. Radivojac
- Biology, Medicine
- Genome Biology
- 3 January 2016
BackgroundA major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of… Expand
SoyDB: a knowledge database of soybean transcription factors
BackgroundTranscription factors play the crucial rule of regulating gene expression and influence almost all biological processes. Systematically identifying and annotating transcription factors can… Expand
NNcon: improved protein contact map prediction using 2D-recursive neural networks
Protein contact map prediction is useful for protein folding rate prediction, model selection and 3D structure prediction. Here we describe NNcon, a fast and reliable contact map prediction server… Expand
Large-scale prediction of disulphide bridges using kernel methods, two-dimensional recursive neural networks, and weighted graph matching.
The formation of disulphide bridges between cysteines plays an important role in protein folding, structure, function, and evolution. Here, we develop new methods for predicting disulphide bridges in… Expand