> Tag > Links tagged with 'molecular models'

Links tagged with 'molecular models'

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Found 177 links

Displaying 15 links

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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

PAComplexTool Content

http://PAcomplex.life.nctu.edu.tw [open in a new window]

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Protein > Networks & Interactions, Pathways and Enzymes

PAComplex is a web server for inferring peptide antigen families and binding models from T-cell receptor-peptide MHC complexes.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
PAComplex: a web server to infer peptide antigen families and binding models from TCR-pMHC complexes20111
NAR Web Server Issue 2011
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tagsantigen receptors histocompatibility antigens class i molecular models mycoplasma pneumonia peptides pol gene products ribosomal proteins

PBETool Content

http://bioinformatics.univ-reunion.fr/PBE/ [open in a new window]

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Protein > 3-D Structure Comparison

Protein Blocks Expert (PBE) uses a structural alphabet of short structural motifs to compare protein structures. PBE uses as its structural alphabet a set of protein blocks derived from structurally aligned homologous proteins present in the PALI Database.

links directory index: 252
TitlePublication YearGoogle Scholar Citation Count
Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet200643
New assessment of a structural alphabet200541
Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks2000168
NAR Web Server Issue 2006
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tagsamino acid motifs artificial intelligence bayes theorem cluster analysis computer simulation factual databases forecasting ligases molecular models neural networks (computer) peptide fragments protein conformation protein databases protein folding protein sequence analysis proteins secondary protein structure sequence alignment ubiquitins

PBILTool Content

http://pbil.univ-lyon1.fr/ [open in a new window]

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Education > Directories and Portals

Pole Bio-Informatique Lyonnais (PBIL) provides access to sequence databanks (EMBL, GenBank, SWISS-PROT, PIR) and to many tools of nucleic acid and protein sequence analyses.

links directory index: 40
TitlePublication YearGoogle Scholar Citation Count
Integrated databanks access and sequence/structure analysis services at the PBIL200340
NAR Web Server Issue 2003
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tagsdna sequence analysis genetic databases molecular models nucleic acids protein conformation protein sequence analysis proteins rna sequence analysis secondary protein structure sequence alignment sequence homology systems integration

PCETool Content

http://bioserv.rpbs.jussieu.fr/Help/PCE.html [open in a new window]

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Protein > Biochemical Features

PCE (Protein Continuum Electrostatics) is an interface to electrostatic potentials and pKa calculations using the MEAD package.

links directory index: 32
TitlePublication YearGoogle Scholar Citation Count
PCE: web tools to compute protein continuum electrostatics200532
NAR Web Server Issue 2005
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tagshydrogen-ion concentration molecular models muramidase proteins static electricity

Pcons.netTool Content

http://pcons.net/ [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching and Classification

Pcons.net is a protein structure prediction meta server that provides automated tools for protein structure prediction and analysis using a consensus approach.

links directory index: 253
TitlePublication YearGoogle Scholar Citation Count
Pcons.net: protein structure prediction meta server200737
Identification of correct regions in protein models using structural, alignment, and consensus information200693
Pcons5: combining consensus, structural evaluation and fold recognition scores200551
Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller200372
NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence animals automatic data processing automation computational biology computer simulation consensus sequence humans molecular models molecular sequence data neural networks (computer) protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins roc curve secondary protein structure sensitivity and specificity sequence alignment statistical models tertiary protein structure

PDBSiteScanTool Content

http://wwwmgs.bionet.nsc.ru/mgs/systems/fastprot/pdbsitescan.html [open in a new window]

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Protein > 3-D Structural Features

PDBSiteScan takes a PDB file as input, and searches for stuctural matches with the PDBSite set of known functional sites.

links directory index: 63
TitlePublication YearGoogle Scholar Citation Count
PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins200463
NAR Web Server Issue 2004
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tagsbinding sites catalytic domain hydrolases intracellular signaling peptides and proteins molecular models oncogene proteins post-translational protein processing proteins tertiary protein structure

PEP-FOLDTool Content

http://bioserv.rpbs.univ-paris-diderot.fr/PEP-FOLD [open in a new window]

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Protein > 3-D Structure Prediction

PEP-FOLD uses a hidden Markov model-derived structural alphabet for de novo modeling of 3D conformations of peptides between 9-25 amino acids in aqueous solution. Updates to PEP-FOLD allow for modeling of linear and disulphide bonded cyclic peptides with 9-36 amino acids using benchmarked peptides.

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links directory index: 43
TitlePublication YearGoogle Scholar Citation Count
PEP-FOLD: an online resource for de novo peptide structure prediction200943
NAR Web Server Issue 2009NAR Web Server Issue 2012
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tagsalgorithms internet molecular models peptides protein conformation protein sequence analysis reproducibility of results software user-computer interface

pepMMsMIMICTool Content

http://mms.dsfarm.unipd.it/pepMMsMIMIC [open in a new window]

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Other Molecules > Compounds
Protein > 3-D Structure Comparison

pepMMsMIMIC is a peptidomimetic compound virtual screening tool based on a multi-confromers 3D-similarity search strategy. Using as input the 3D structure of a peptide bound to a protein, pepMMsMIMIC suggests which chemical structures are able to mimic the protein-protein recognitiuon of this natural peptide using pharmacophore and shape similarity techniques.

This content is being maintained by matteofloris.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
Swimming into peptidomimetic chemical space using pepMMsMIMIC20113
NAR Web Server Issue 2011
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tagsbiomimetic materials chemoinformatics drug design molecular models peptides peptidomimetics protein conformation virtual screening

pevoSOARTool Content

http://sts.bioengr.uic.edu/pevosoar/ [open in a new window]

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Protein > 3-D Structure Comparison

pvSOAR takes a PDB ID or structure file as input, and searches for other proteins with surface regions that are similar to the query structure.

links directory index: 55
TitlePublication YearGoogle Scholar Citation Count
pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins200455
NAR Web Server Issue 2004
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tagsamino acids binding sites molecular models protein conformation protein databases proteins

PfamDatabase Content

http://pfam.sanger.ac.uk/ [open in a new window]

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Protein > Databases

Pfam is a database of protein families and domains. The database uses HMMER3, the latest version of the popular profile hidden Markov model package. Pfam release 24.0 contains 11,912 families.

links directory index: 11859
TitlePublication YearGoogle Scholar Citation Count
The Pfam protein families database.2012212
The Pfam protein families database.20101375
The Pfam protein families database.20081524
Pfam: clans, web tools and services.20061648
The Pfam protein families database.20042639
The Pfam protein families database.20022079
The Pfam protein families database.20001281
Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.1999545
Pfam: multiple sequence alignments and HMM-profiles of protein domains.1998556
NAR Database Issue 2010
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tagsalgorithms amino acid sequence amino acid sequence homology animals archaeal genome binding sites caenorhabditis elegans computational biology computer communication networks computer graphics encyclopedias as topic factual databases fungal genome genome genomics humans information storage and retrieval internet macromolecular substances markov chains molecular evolution molecular models molecular sequence data multigene family nucleic acid databases phylogeny protein conformation protein databases protein sequence analysis proteins quality control secondary protein structure sequence alignment software statistics as topic tertiary protein structure user-computer interface

PfoldTool Content

http://www.daimi.au.dk/~compbio/pfold [open in a new window]

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RNA > Structure Prediction, Visualization, and Design

The Pfold server takes an alignment of RNA sequences as input and predicts a common secondary structure.

links directory index: 560
TitlePublication YearGoogle Scholar Citation Count
Pfold: RNA secondary structure prediction using stochastic context-free grammars2003280
RNA secondary structure prediction using stochastic context-free grammars and evolutionary history1999280
NAR Web Server Issue 2003
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tagsalgorithms bacterial rna base sequence biological evolution catalytic rna computational biology computer simulation endoribonucleases molecular evolution molecular models molecular sequence data nucleic acid conformation nucleic acid sequence homology probability reproducibility of results ribonuclease p rna rna sequence analysis sequence alignment stochastic processes time factors

PhobiusTool Content

http://phobius.sbc.su.se/ [open in a new window]

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Protein > 2-D Structure Prediction
Protein > Localization and Targeting

Phobius is a combined transmembrane topology and signal peptide predictor. The server also allows for constrained and homology-enriched predictions.

This content is being maintained by lukall.

links directory index: 863
TitlePublication YearGoogle Scholar Citation Count
Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server2007176
An HMM posterior decoder for sequence feature prediction that includes homology information2005121
A combined transmembrane topology and signal peptide prediction method2004566
NAR Web Server Issue 2007
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tagsalgorithms artificial intelligence computational biology computer simulation cytoplasm markov chains membrane proteins molecular models probability programming languages protein conformation protein databases protein sorting signals proteomics secondary protein structure statistical models theoretical models

PhosfinderTool Content

http://phosfinder.bio.uniroma2.it [open in a new window]

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Protein > 3-D Structural Features

Phosfinder uses a structural comparison algorithm to identify phosphate binding sites in protein structures. It scans a query structure in PDB format against a set of known 3D phosphate binding motifs and outputs a visual display of the predicted binding sites on the query protein structure.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
Phosfinder: a web server for the identification of phosphate-binding sites on protein structures20111
NAR Web Server Issue 2011
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tagsbinding sites molecular models phosphates protein conformation proteins

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

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