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Protocols

INTREPID specifications

Information


Unique identifier OMICS_07168
Name INTREPID
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Kimmen Sjölander

Information


Unique identifier OMICS_07168
Name INTREPID
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Kimmen Sjölander

Publications for INTREPID

INTREPID citations

 (13)
call_split

Inferring joint sequence structural determinants of protein functional specificity

2018
eLife
PMCID: 5770160
PMID: 29336305
DOI: 10.7554/eLife.29880.030
call_split See protocol

[…] ple. However, several factors complicate comparisons to BPPS-SIPRIS. First, a fair number of published FDR methods are no longer available as source code, executables or over the world wide web (e.g. INTREPID [] and MINER []). Second, many FDR methods (e.g. GroupSim []) require user-provided input, such as an MSA, a phylogenetic tree, or prespecified categories with corresponding sequence assignme […]

library_books

Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods

2015
Int J Mol Sci
PMCID: 4691145
PMID: 26694353
DOI: 10.3390/ijms161226202

[…] s can be broadly categorised into methods that utilize machine learning (Multi-RELIEF [], TargetS [], LigandRF [], and OMSL []), methods that utilize only position-specific scoring matrices or PSSMs (INTREPID [], DISCERN [], ConSurf [], and ConFunc []) and graph-based methods such as Conditional Random Field (CRF) []. The advent of including machine learning-based strategies into sequence-based me […]

library_books

Prediction of distal residue participation in enzyme catalysis

2015
PMCID: 4420525
PMID: 25627867
DOI: 10.1002/pro.2648

[…] oretical Microscopic Titration Curves (THEMATICS), using the method of Wei. POOL calculations were performed as described previously. Unless otherwise noted, input features include THEMATICS metrics, INTREPID evolutionary scores and ConCavity surface geometry features. INTREPID scores were obtained using the Berkeley phylogenomics web server. The structure-only version of ConCavity was used.The Li […]

library_books

Biochemical functional predictions for protein structures of unknown or uncertain function

2015
Comput Struct Biotechnol J
PMCID: 4372640
PMID: 25848497
DOI: 10.1016/j.csbj.2015.02.003

[…] e methods primarily utilize sequence alignments but sometimes also incorporate 3D structures . Evolutionary Trace and INformation-theoretic TREe traversal for Protein functional site IDentification (INTREPID) , examine a protein in its phylogenetic context and the evolutionary history of each amino acid in a protein sequence to assign a score to each amino acid. Evolutionary Trace analyzes the co […]

library_books

Rapid Catalytic Template Searching as an Enzyme Function Prediction Procedure

2013
PLoS One
PMCID: 3651201
PMID: 23675414
DOI: 10.1371/journal.pone.0062535

[…] % or more, with some high accuracy methods recommending 60% identity , . Other approaches, which are largely phylogenetic in nature, include Hidden Markov Model (HMM) methods , , Evolutionary Trace , INTREPID , Phylofacts , , and Bayesian Monte Carlo inference . that combine sequence and structural information include EFICAz , , SOIPPA –, DISCERN , PevoSOAR , and AnnoLite and can provide improve […]

library_books

Protein function annotation with Structurally Aligned Local Sites of Activity (SALSAs)

2013
BMC Bioinformatics
PMCID: 3584854
PMID: 23514271
DOI: 10.1186/1471-2105-14-S3-S13

[…] ue predictions were made using POOL [,]. Input features for each residue in a given structure include: electrostatics information, as contained in THEMATICS metrics [,]; phylogenetic information from INTREPID [,]; and geometric information from ConCavity (structure only version) []. The top-ranked residues in the POOL output constitute the functional site prediction. Cut-off limits are specified f […]

Citations

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INTREPID institution(s)
Department of Computer Science, University of California, Berkeley, USA

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