Text Mining for Protein Docking

Text as data: Using text-based features for proteins representation and for computational prediction of their characteristics

(2015) Hagit Shatkay et al.   METHODS

Protein–protein interaction predictions using text mining methods

(2015) Nikolas Papanikolaou et al.   METHODS

Protein-Protein Docking: From Interaction to Interactome

(2014) Ilya A. Vakser   BIOPHYSICAL JOURNAL

Scoring functions for protein–protein interactions

(2013) Iain H Moal et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis

(2013) Philipp Blohm et al.   NUCLEIC ACIDS RESEARCH

Activities at the Universal Protein Resource (UniProt)

(2013)   NUCLEIC ACIDS RESEARCH

Docking, scoring, and affinity prediction in CAPRI

(2013) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Literature mining of host–pathogen interactions: comparing feature-based supervised learning and language-based approaches

(2012) Thanh Thieu et al.   BIOINFORMATICS

A text-mining system for extracting metabolic reactions from full-text articles

(2012) Jan Czarnecki et al.   BMC BIOINFORMATICS

Automated extraction and semantic analysis of mutation impacts from the biomedical literature

(2012) Nona Naderi et al.   BMC GENOMICS

Text-mining solutions for biomedical research: enabling integrative biology

(2012) Dietrich Rebholz-Schuhmann et al.   NATURE REVIEWS GENETICS

Text Mining Improves Prediction of Protein Functional Sites

(2012) Karin M. Verspoor et al.   PLoS One

Text Mining for Literature Review and Knowledge Discovery in Cancer Risk Assessment and Research

(2012) Anna Korhonen et al.   PLoS One

Templates are available to model nearly all complexes of structurally characterized proteins

(2012) P. J. Kundrotas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PIE the search: searching PubMed literature for protein interaction information

(2011) Sun Kim et al.   BIOINFORMATICS

Classifying protein-protein interaction articles using word and syntactic features

(2011) Sun Kim et al.   BMC BIOINFORMATICS

PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries

(2011) Adriano Barbosa-Silva et al.   BMC BIOINFORMATICS

LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships

(2010) Adriano Barbosa-Silva et al.   BMC BIOINFORMATICS

Literature curation of protein interactions: measuring agreement across major public databases

(2010) A. L. Turinsky et al.   Database-The Journal of Biological Databases and Curation

Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I2D

(2009) Yun Niu et al.   BIOINFORMATICS

Protein–protein interaction extraction by leveraging multiple kernels and parsers

(2009) Makoto Miwa et al.   INTERNATIONAL JOURNAL OF MEDICAL INFORMATICS

DOCKGROUND protein-protein docking decoy set

(2008) S. Liu et al.   BIOINFORMATICS