PROSPER: An Integrated Feature-Based Tool for Predicting Protease Substrate Cleavage Sites

FunSAV: Predicting the Functional Effect of Single Amino Acid Variants Using a Two-Stage Random Forest Model

(2012) Mingjun Wang et al.   PLoS One

Predicting Residue-Residue Contacts and Helix-Helix Interactions in Transmembrane Proteins Using an Integrative Feature-Based Random Forest Approach

(2011) Xiao-Feng Wang et al.   PLoS One

Redesigning allosteric activation in an enzyme

(2011) S. Rana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources

(2010) Marcin J. Mizianty et al.   BIOINFORMATICS

Multilevel support vector regression analysis to identify condition-specific regulatory networks

(2010) Li Chen et al.   BIOINFORMATICS

DROP: an SVM domain linker predictor trained with optimal features selected by random forest

(2010) Teppei Ebina et al.   BIOINFORMATICS

Cascleave: towards more accurate prediction of caspase substrate cleavage sites

(2010) Jiangning Song et al.   BIOINFORMATICS

Prediction of protease substrates using sequence and structure features

(2010) David T. Barkan et al.   BIOINFORMATICS

Pripper: prediction of caspase cleavage sites from whole proteomes

(2010) Mirva Piippo et al.   BMC BIOINFORMATICS

Who gets cut during cell death?

(2010) Francis Impens et al.   CURRENT OPINION IN CELL BIOLOGY

Musite, a Tool for Global Prediction of General and Kinase-specific Phosphorylation Sites

(2010) Jianjiong Gao et al.   MOLECULAR & CELLULAR PROTEOMICS

Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products

(2010) Oded Kleifeld et al.   NATURE BIOTECHNOLOGY

Complementary positional proteomics for screening substrates of endo- and exoproteases

(2010) Petra Van Damme et al.   NATURE METHODS

Proteome-wide analysis of protein carboxy termini: C terminomics

(2010) Oliver Schilling et al.   NATURE METHODS

High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions

(2010) Phaedra Agius et al.   PLoS Computational Biology

BIOINFORMATIC APPROACHES FOR PREDICTING SUBSTRATES OF PROTEASES

(2010) JIANGNING SONG et al.   Journal of Bioinformatics and Computational Biology

The crystal structure of caspase-6, a selective effector of axonal degeneration

(2009) Renato Baumgartner et al.   BIOCHEMICAL JOURNAL

M are better than one: an ensemble-based motif finder and its application to regulatory element prediction

(2009) Chen Yanover et al.   BIOINFORMATICS

A multi-factor model for caspase degradome prediction

(2009) Lawrence JK Wee et al.   BMC GENOMICS

Intrinsic Protein Disorder and Interaction Promiscuity Are Widely Associated with Dosage Sensitivity

(2009) Tanya Vavouri et al.   CELL

Human Caspases: Activation, Specificity, and Regulation

(2009) Cristina Pop et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Proteome-wide Substrate Analysis Indicates Substrate Exclusion as a Mechanism to Generate Caspase-7VersusCaspase-3 Specificity

(2009) Dieter Demon et al.   MOLECULAR & CELLULAR PROTEOMICS

Structural and kinetic determinants of protease substrates

(2009) John C Timmer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

MEROPS: the peptidase database

(2009) Neil D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

(2009) J. Chen et al.   NUCLEIC ACIDS RESEARCH

Computational Identification of Protein Methylation Sites through Bi-Profile Bayes Feature Extraction

(2009) Jianlin Shao et al.   PLoS One

Prodepth: Predict Residue Depth by Support Vector Regression Approach from Protein Sequences Only

(2009) Jiangning Song et al.   PLoS One

SitePredicting the cleavage of proteinase substrates

(2009) Jelle Verspurten et al.   TRENDS IN BIOCHEMICAL SCIENCES

Detection of Alpha-Rod Protein Repeats Using a Neural Network and Application to Huntingtin

(2009) Gareth A. Palidwor et al.   PLoS Computational Biology

Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data

(2009) Yvonne JK Edwards et al.   GENOME BIOLOGY

HSEpred: predict half-sphere exposure from protein sequences

(2008) Jiangning Song et al.   BIOINFORMATICS

Protease substrate site predictors derived from machine learning on multilevel substrate phage display data

(2008) Ching-Tai Chen et al.   BIOINFORMATICS

Prediction of disordered regions in proteins based on the meta approach

(2008) T. Ishida et al.   BIOINFORMATICS

Sequence based residue depth prediction using evolutionary information and predicted secondary structure

(2008) Hua Zhang et al.   BMC BIOINFORMATICS

Global Sequencing of Proteolytic Cleavage Sites in Apoptosis by Specific Labeling of Protein N Termini

(2008) Sami Mahrus et al.   CELL

Global Mapping of the Topography and Magnitude of Proteolytic Events in Apoptosis

(2008) Melissa M. Dix et al.   CELL

Allosteric Regulation of Proteases

(2008) Patrick Hauske et al.   CHEMBIOCHEM

Activated caspase-6 and caspase-6-cleaved fragments of huntingtin specifically colocalize in the nucleus

(2008) Simon C. Warby et al.   HUMAN MOLECULAR GENETICS

Analysis of Protein Processing by N-terminal Proteomics Reveals Novel Species-specific Substrate Determinants of Granzyme B Orthologs

(2008) Petra Van Damme et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteome-derived, database-searchable peptide libraries for identifying protease cleavage sites

(2008) Oliver Schilling et al.   NATURE BIOTECHNOLOGY

FFPred: an integrated feature-based function prediction server for vertebrate proteomes

(2008) A. E. Lobley et al.   NUCLEIC ACIDS RESEARCH

PMAP: databases for analyzing proteolytic events and pathways

(2008) Yoshinobu Igarashi et al.   NUCLEIC ACIDS RESEARCH

The Degradome database: mammalian proteases and diseases of proteolysis

(2008) V. Quesada et al.   NUCLEIC ACIDS RESEARCH

Tight Regulation of Unstructured Proteins: From Transcript Synthesis to Protein Degradation

(2008) J. Gsponer et al.   SCIENCE

Structural disorder serves as a weak signal for intracellular protein degradation

(2007) P. Tompa et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS