> Tag > Links tagged with 'protein binding'

Links tagged with 'protein binding'

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Found 53 links

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NORSpTool Content

http://cubic.bioc.columbia.edu/services/NORSp/ [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction

NORSp (predictor of NOn-Regular Secondary Structure) is a tool for predicting disordered regions in proteins.

links directory index: 251
TitlePublication YearGoogle Scholar Citation Count
NORSp: Predictions of long regions without regular secondary structure2003106
Loopy proteins appear conserved in evolution2002145
NAR Web Server Issue 2003
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tagsamino acids computational biology conserved sequence genetic transcription hydrogen bonding molecular evolution molecular models pliability protein binding protein databases protein folding protein sequence analysis proteins proteome secondary protein structure software design solvents structure-activity relationship

oGNMTool Content

http://ignm.ccbb.pitt.edu/GNM_Online_Calculation.htm [open in a new window]

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Protein > Molecular Dynamics and Docking

Online Guassian Network Model (oGNM) calculates the equilibrium dynamics of any structure submitted in PDB format, using the Gaussian Network Model (GNM), a network model for representing biomolecules.

links directory index: 795
TitlePublication YearGoogle Scholar Citation Count
oGNM: online computation of structural dynamics using the Gaussian Network Model200651
iGNM: a database of protein functional motions based on Gaussian Network Model200587
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential1997657
NAR Web Server Issue 2006
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tagsalgorithms binding sites chemical models computational biology computer simulation molecular models molecular structure motion normal distribution nucleic acid conformation oligonucleotides protein binding protein conformation protein databases protein folding protein sequence analysis proteins sequence alignment statistical models structure-activity relationship thermodynamics x-ray crystallography

ORegAnnoDatabase Content

http://www.oreganno.org/ [open in a new window]

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DNA > Annotations
DNA > Databases
DNA > Sequence Polymorphisms
Expression > Gene Regulation
Human Genome > Annotations
Human Genome > Sequence Polymorphisms

The Open REGulatory ANNOtation database (ORegAnno) is a collection of literature-curated regulatory regions, transcription factor binding sites (TFBS) and regulatory mutations.

This content is being maintained by obigriffith.

links directory index: 145
TitlePublication YearGoogle Scholar Citation Count
ORegAnno: an open-access community-driven resource for regulatory annotation200873
ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation200672
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external linksLink on Wikipedia
tagsanimals binding sites database management systems documentation gene expression regulation genetic databases genetic promoter regions genetic variation humans natural language processing nucleic acid databases periodicals as topic protein binding transcription factors transcriptional regulatory elements

PAPTool Content

http://bioinformatics.wustl.edu/webTools/portalModule/PromoterSearch.do [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Promoter Analysis Pipeline (PAP) can identify potential transcriptional regulators for sets of co-expressed genes and identify potential regulatory targets of transcription factors.

links directory index: 72
TitlePublication YearGoogle Scholar Citation Count
PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis200719
A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles200653
NAR Web Server Issue 2007
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tagsalgorithms animals cell proliferation cholesterol chromatin immunoprecipitation computational biology conserved sequence gene expression profiling gene expression regulation genetic databases genetic models genetic promoter regions genetic transcription humans mice protein binding transcription factors

PepStrTool Content

http://www.imtech.res.in/raghava/pepstr/ [open in a new window]

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Other Molecules > Peptides
Protein > Sequence Features

The Pepstr server predicts the tertiary structure of small peptides with sequence length varying between 7 to 25 residues. The prediction strategy is based on the realization that β-turn is an important and consistent feature of small peptides in addition to regular structures. Thus, the methods uses both the regular secondary structure information predicted from PSIPRED and β-turns information predicted from BetaTurns.

This content is being maintained by raghavagps.

links directory index: 17
TitlePublication YearGoogle Scholar Citation Count
PEPstr: a de novo method for tertiary structure prediction of small bioactive peptides200717
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tagsbeta-turns bioactive ligands monte carlo method peptides protein binding tertiary protein structure tertiary structure prediction

PI2PETool Content

http://pipe.scs.fsu.edu/ [open in a new window]

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Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Networks & Interactions, Pathways and Enzymes

PI2PE (Protein Interface/Interior Prediction Engine) consists of three predictors (WESA, cons-PPISP, and DISPLAR) for predicting solvent accessibility and interface residues from the structure of a protein-binding or DNA-binding protein.

links directory index: 473
TitlePublication YearGoogle Scholar Citation Count
PI2PE: protein interface/interior prediction engine200718
DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces200751
Prediction of solvent accessibility and sites of deleterious mutations from protein sequence200549
Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data2005111
Fold recognition and accurate query-template alignment by a combination of PSI-BLAST and threading200136
Prediction of protein interaction sites from sequence profile and residue neighbor list2001208
NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence amino acid sequence homology amino acids animals artificial intelligence binding sites biomolecular nuclear magnetic resonance computational biology computer simulation dna dna-binding proteins factual databases genomic library hydrophobic and hydrophilic interactions membrane proteins molecular conformation molecular models molecular sequence data mutation mycoplasma neural networks (computer) open reading frames prions protein binding protein conformation protein sequence analysis proteins quaternary protein structure reproducibility of results rna-binding proteins saccharomyces cerevisiae secondary protein structure sequence alignment solvents

POPSTool Content

http://mathbio.nimr.mrc.ac.uk/wiki/POPS [open in a new window]

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Protein > 3-D Structural Features

Parameter OPtimised Surfaces (POPS) is an algorithm to calculate accessible surfaces areas at atomic and residue level.

links directory index: 114
TitlePublication YearGoogle Scholar Citation Count
POPS: A fast algorithm for solvent accessible surface areas at atomic and residue level200349
Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome200265
NAR Web Server Issue 2003
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tagsalgorithms amino acids hydrophobic and hydrophilic interactions macromolecular substances molecular models molecular structure nucleic acid conformation nucleic acids protein binding protein conformation proteins ribosomal proteins ribosomal rna ribosomes solvents time factors transfer rna

PredUsTool Content

http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:PredUs [open in a new window]

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Protein > Networks & Interactions, Pathways and Enzymes

PredUs is a web server for the prediction of protein-protein interfaces. The method predicts protein-protein interfaces of a given monomeric query protein using its close and remote structural neighbors.

This content is being maintained by cliffzhang.

links directory index: 27
TitlePublication YearGoogle Scholar Citation Count
PredUs: a web server for predicting protein interfaces using structural neighbors20113
Protein interface conservation across structure space201024
NAR Web Server Issue 2011
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tagsalgorithms artificial intelligence binding sites computational biology conserved sequence molecular models multiprotein complexes protein binding protein conformation protein databases protein interaction domains and motifs protein interaction mapping protein structural homology proteins sequence alignment surface properties systems biology

PREP SuiteTool Content

http://prep.unl.edu/ [open in a new window]

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Model Organisms > Plants
RNA > Motifs

The PREP (Predictive RNA Editors for Plants) suite predicts sites of RNA editing based on the principle that editing in plant organelles increases the conservation of proteins across species. Predictors for mitochondrial genes, chloroplast genes, and alignments input by the user are included.

This content is being maintained by jpmower.

links directory index: 49
TitlePublication YearGoogle Scholar Citation Count
The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments200911
PREP-Mt: predictive RNA editor for plant mitochondrial genes200538
NAR Web Server Issue 2009
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tagsamino acid sequence amino acid sequence homology base sequence binding sites chloroplast rna chloroplasts computational biology conserved sequence cytidine dna dna sequence analysis mitochondrial genes mitochondrial proteins molecular sequence data phylogeny plant dna plant gene expression regulation plant genes plant genome plant proteins protein binding protein databases reproducibility of results rna rna editing rna sequence analysis sensitivity and specificity sequence alignment statistical models

ProMateusTool Content

http://bioportal.weizmann.ac.il/promate/ [open in a new window]

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Protein > 3-D Structural Features
Protein > Networks & Interactions, Pathways and Enzymes

ProMateus extends ProMate, a protein binding site predictor, and allows the user to suggest new features that might improve the prediction of the binding site locations.

links directory index: 251
TitlePublication YearGoogle Scholar Citation Count
ProMateus--an open research approach to protein-binding sites analysis200718
ProMate: a structure based prediction program to identify the location of protein-protein binding sites2004233
NAR Web Server Issue 2007
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tagsalgorithms binding sites computational biology dna factual databases molecular models protein binding protein conformation proteins secondary protein structure surface properties

ProPred1Tool Content

http://www.imtech.res.in/raghava/propred1 [open in a new window]

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Protein > Domains and Motifs

The ProPred-I is an on-line service for identifying the MHC Class-I binding regions in antigens. It implements matrices for 47 MHC Class-I alleles, proteasomal and immunoproteasomal models. The main aim of this server is to help users in identifying the promiscuous regions.

This content is being maintained by raghavagps.

links directory index: 106
TitlePublication YearGoogle Scholar Citation Count
ProPred1: prediction of promiscuous MHC Class-I binding sites2003106
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tagsalleles antigen presentation antigens binding peptides binding sites cysteine endopeptidases histocompatibility antigens class i immunoproteasome cleavage site macromolecular substances major histocompatibility complex MHC I multienzyme complexes oligopeptides peptides prediction proteasome cleavage site proteasome endopeptidase complex protein binding protein databases protein sequence analysis

ReadOutTool Content

http://gibk26.bio.kyutech.ac.jp/jouhou/readout/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > 3-D Structural Features

Readout is a server for the calculation of direct and indirect readout energy Z-scores which estimate the degree of sequence specificity of the protein-DNA complex. Readout can be useful for checking the quality of protein-DNA interactions in three dimensional (3D) structures.

links directory index: 318
TitlePublication YearGoogle Scholar Citation Count
ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition200628
Intermolecular and intramolecular readout mechanisms in protein-DNA recognition200487
Specificity of protein-DNA recognition revealed by structure-based potentials: symmetric/asymmetric and cognate/non-cognate binding200262
Structure-based prediction of DNA target sites by regulatory proteins1999141
NAR Web Server Issue 2006
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tagsbacterial proteins base sequence binding sites biological models dimerization dna dna primers dna-binding proteins endonucleases gene expression regulation genetic promoter regions glucocorticoid receptors hydrogen bonding macromolecular substances metalloproteins molecular models nucleic acid conformation protein binding protein conformation protein kinases protein subunits proteins repressor proteins saccharomyces cerevisiae proteins tertiary protein structure thermodynamics type ii site-specific deoxyribonucleases viral proteins viral regulatory and accessory proteins water zinc fingers

RNAcontextTool Content

http://www.cs.toronto.edu/~hilal/rnacontext/ [open in a new window]

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Protein > 3-D Structural Features
Protein > Domains and Motifs

RNAcontext: a new motif-finding method designed to elucidate RNA-binding protein (RBP) specific sequence and structural preferences with greater accuracy than existing approahces.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins20109
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tagsalgorithms amino acid motifs amino acid sequence area under curve base sequence binding sites genetic models messenger rna nucleic acid conformation protein binding protein conformation protein databases rna-binding proteins statistical models
setsUniversity of Toronto

Services from Zhou LaboratoryResource Content

http://cssb.biology.gatech.edu/skolnick/people/zhou.html [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
Protein > Networks & Interactions, Pathways and Enzymes

Tools from the Zhou laboratory including predictors of transmembrane topology (THUMBUP, UMDHMM-TMHP, TUPS); prediction/analysis tools for tertiary structure (SPARKS2, SP3); and, prediction/analysis tools for interactions (DMONOMER, DLOOP, DMUTANT, DCOMPLEX, DDNA, TCD, DOGMA).

links directory index: 1058
TitlePublication YearGoogle Scholar Citation Count
Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations200520
Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments2005136
Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential200473
Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition2004135
A physical reference state unifies the structure-derived potential of mean force for protein folding and binding200492
Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method200360
Folding rate prediction using total contact distance2002139
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction2002403
NAR Web Server Issue 2005
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tagsalgorithms amino acid sequence amino acid sequence homology amino acids antigen-antibody complex binding sites biological evolution chemical models computational biology dimerization factual databases hydrogen bonding kinetics markov chains mathematics membrane proteins molecular evolution molecular structure peptide fragments peptide library plant proteins probability protein binding protein conformation protein databases protein folding protein sequence analysis proteins regression analysis reproducibility of results secondary protein structure sensitivity and specificity sequence alignment statistical models statistics as topic tertiary protein structure theoretical models thermodynamics time factors

SH3-HunterTool Content

http://cbm.bio.uniroma2.it/SH3-Hunter/ [open in a new window]

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Protein > Domains and Motifs
Protein > Networks & Interactions, Pathways and Enzymes

SH3-Hunter identifies putative SH3 domain interaction sites on protein sequences.

This content is being maintained by enricoferraro.

links directory index: 102
TitlePublication YearGoogle Scholar Citation Count
SH3-Hunter: discovery of SH3 domain interaction sites in proteins200711
A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity200617
SH3-SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family200074
NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence animals artificial intelligence automated pattern recognition binding sites chemical models computational biology computer simulation factual databases humans ligands molecular models molecular sequence data multigene family neural networks (computer) peptide fragments peptide library peptides probability protein binding protein interaction mapping protein sequence analysis proteins proteome sensitivity and specificity sequence alignment src homology domains structure-activity relationship substrate specificity tertiary protein structure

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