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NLProt specifications


Unique identifier OMICS_20064
Name NLProt
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes


Unique identifier OMICS_20064
Name NLProt
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes


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Publications for NLProt

NLProt citations


Text Mining for Protein Docking

PLoS Comput Biol
PMCID: 4674139
PMID: 26650466
DOI: 10.1371/journal.pcbi.1004630

[…] ns quickly become available online (e.g. through PubMed,, and are a growing resource for automated mining of the PP binding mode. Many applications (PubMed ENTREZ, NLProt, MedMiner, etc.) utilizing TM techniques have been developed to improve access to the published knowledge []. TM converts textual information into database content and complex networks, facilit […]


A review on computational systems biology of pathogen–host interactions

Front Microbiol
PMCID: 4391036
PMID: 25914674
DOI: 10.3389/fmicb.2015.00235

[…] a host and pathogen protein, features that make use of the negation signaling keywords were also designed. The protein and gene names, as well as the corresponding organisms were tagged by using the NLProt software (). A set of dictionaries for interaction keywords, experimental keywords, negation keywords, PHI-keywords, host names, pathogen names, and uncertainty keywords was manually compiled. […]


Systems Biology Elucidates Common Pathogenic Mechanisms between Nonalcoholic and Alcoholic Fatty Liver Disease

PLoS One
PMCID: 3596348
PMID: 23516571
DOI: 10.1371/journal.pone.0058895
call_split See protocol

[…] occurrences for AFLD, and 868 papers and 2217 co-occurrences for NAFLD. The query involves retrieving extensible markup language (XML) PubMed abstracts for PMID list, passing XML PubMed abstracts for NLPROT analysis (a tool for finding protein names in natural language text), and tagging protein names and performing co-occurrences analyses. After carrying out terms' tagging, a total of 228 gene/pr […]


Correction: A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein protein interaction literature

BMC Bioinformatics
PMCID: 3436857
DOI: 10.1186/1471-2105-13-180

[…] racts; this can be seen by comparing the performance of VTT0 (no NER tools) with VTT1 (using ABNER) in Table 5. However, there are only minor gains in performance by applying the additional NER tools NLProt [3] and OSCAR 3 [4] to abstracts; this can be seen by comparing the performance of VTT1 (using ABNER) with VTT3 (using ABNER, NLProt and OSCAR 3) shown in the corrected Tables 5 and 7.2. Includ […]


A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein protein interaction literature

BMC Bioinformatics
PMCID: 3269935
PMID: 22151823
DOI: 10.1186/1471-2105-12-S8-S12
call_split See protocol

[…] we are interested in the entity count features that can best discriminate documents relevant for PPI (positive) from irrelevant ones (negative). For that purpose, we utilized the NER tools ABNER [,], NLProt [] and OSCAR 3 [,] and compiled dictionaries from the BRENDA (enzymes) [,] and ChEBI (chemical compounds) [] databases, as well as the PSI-MI ontology (experimental methods) [].With each one of […]


The Protein Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio ontology concepts to full text

BMC Bioinformatics
PMCID: 3269938
PMID: 22151929
DOI: 10.1186/1471-2105-12-S8-S3

[…] rotein Interaction, members of Team 81 were interested in investigating the advantages of using full-text data on the classification. Team 81 utilized the following NER tools and dictionaries: ABNER, NLProt, Oscar 3, ChEBI (Chemical names), PSI-MI, MeSH terms, and BRENDA enzyme names. Team 81 also used the output of their Interaction Methods Task pipeline as an additional annotation tool. While th […]


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NLProt institution(s)
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA; Columbia University Center for Computational Biology and Bioinformatics (C2B2), Russ Berrie Pavilion, New York, NY, USA; Institute of Physical Biochemistry, University Witten/Herdecke, Witten, Germany
NLProt funding source(s)
Supported by the grants RO1-GM63029-01 from the National Institutes of Health (NIH), R01-LM07329-01 from the National Library of Medicine (NLM) and DBI-0131168 from the National Science Foundation (NSF).

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