Enhanced performance in prediction of protein active sites with THEMATICS and support vector machines (Q36420036)

14 August 2017

Enhanced performance in prediction of protein active sites with THEMATICS and support vector machines (English)

1 reference

14 August 2017

support vector machine

1 reference

2

Ronald J Williams

1 reference

14 August 2017

Wenxu Tong

1

1 reference

14 August 2017

Ying Wei

3

1 reference

14 August 2017

Leonel F Murga

4

1 reference

14 August 2017

Jaeju Ko

5

1 reference

14 August 2017

Mary Jo Ondrechen

6

1 reference

14 August 2017

20 December 2007

1 reference

14 August 2017

1 reference

14 August 2017

17

1 reference

14 August 2017

2

1 reference

14 August 2017

333-341

1 reference

Structure-based activity prediction for an enzyme of unknown function

14 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

Selective prediction of interaction sites in protein structures with THEMATICS.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

Prediction of functional sites in proteins using conserved functional group analysis.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

Future directions in protein function prediction.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

THEMATICS: a simple computational predictor of enzyme function from structure

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

Prediction of functionally important residues based solely on the computed energetics of protein structure.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

Automated analysis of interatomic contacts in proteins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

Three-dimensional profiles: a new tool to identify protein surface similarities.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

Locating and characterizing binding sites on proteins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

Crystal structure of recombinant pea cytosolic ascorbate peroxidase

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

Statistical criteria for the identification of protein active sites using Theoretical Microscopic Titration Curves

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

Evaluation of features for catalytic residue prediction in novel folds

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

Looking at enzymes from the inside out: the proximity of catalytic residues to the molecular centroid can be used for detection of active sites and enzyme-ligand interfaces.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

Enzyme/non-enzyme discrimination and prediction of enzyme active site location using charge-based methods

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

Superfamily active site templates.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

Identification of substrate binding sites in enzymes by computational solvent mapping.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

Using a neural network and spatial clustering to predict the location of active sites in enzymes

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

Analysis of catalytic residues in enzyme active sites

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

Network Analysis of Protein Structures Identifies Functional Residues

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2222725

What we do not know about sequence analysis and sequence databases

5 December 2018

1 reference

12 December 2020

Practical limits of function prediction

1 reference

12 December 2020

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

1 reference

12 December 2020

Crystal structure of cytochrome c peroxidase compound I

1 reference

12 December 2020

Identifiers

DOI

10.1110/PS.073213608

1 reference

14 August 2017

1 reference

14 August 2017

PubMed publication ID

18096640

1 reference