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Links tagged with 'thermodynamics'

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Found 30 links

Displaying 15 links

AD-ENMTool Content

http://enm.lobos.nih.gov

Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Molecular Dynamics and Docking

Analysis of Dynamics of Elastic Network Model (AD-ENM) predicts the conformational changes a given protein structure can undergo.

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tagsactins adenosine triphosphate animals binding sites biophysical phenomena biophysics dictyostelium dna polymerase beta dna-directed rna polymerases elasticity humans kinesin ligands mice molecular conformation molecular models molecular motor proteins myosins nucleotides principal component analysis protein binding protein conformation proton-translocating atpases protozoan proteins secondary protein structure statistical models structure-activity relationship taq polymerase tertiary protein structure theoretical models thermodynamics viral proteins x-ray crystallography

eProbalignTool Content

http://probalign.njit.edu/probalign/login

Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

eProbalign computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities. eProbalign also provides a platform to visualize the alignment, generate images, and manipulate the output.

NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence amino acid sequence homology animals computational biology computer simulation dna genetic databases humans molecular sequence data probability protein sequence analysis sequence alignment software design statistical models temperature thermodynamics

FastContactTool Content

http://structure.pitt.edu/servers/fastcontact/

Protein > Molecular Dynamics and Docking

FastContact is a free energy scoring tool for protein-protein complex structures.

NAR Web Server Issue 2007
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tagsalgorithms amino acids binding sites biological models chemical models computational biology computer simulation hydrogen bonding molecular models protein binding protein conformation protein interaction mapping protein sequence analysis proteins solvents static electricity thermodynamics

FeatureScanTool Content

http://gnaweb.gbf.de/cgi-bin/FeatureScan/FeatureScan.pl

DNA > Structure and Sequence Feature Detection
Sequence Comparison > Similarity Searching

FeatureScan searches for sequence similarity by comparing physico-chemical properties of DNA such as charge, melting enthalpy, conformational parameters, etc.

NAR Web Server Issue 2006
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tagsanimals automated pattern recognition bacterial dna bacterial genes dna dna sequence analysis escherichia coli genetic models genetic promoter regions genomics humans mice nucleic acid sequence homology rats sequence alignment thermodynamics

FOLD-RATETool Content

http://psfs.cbrc.jp/fold-rate/

Protein > Molecular Dynamics and Docking

FOLD-RATE predicts the folding rates of proteins from their amino acid sequences.

NAR Web Server Issue 2006
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tagsamino acid sequence amino acids binding sites chemical models kinetics linear models molecular models mutation protein conformation protein folding protein sequence analysis protein structural homology proteins secondary protein structure solvents statistical models statistics as topic tertiary protein structure thermodynamics

I-Mutant2.0Tool Content

http://gpcr2.biocomp.unibo.it/cgi/predictors/I-Mutant2.0/I-Mutant2.0.cgi

Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking

I-Mutant2.0 is a tool that can predict the effect of a single point mutation on protein stability from protein sequences or protein structures.

NAR Web Server Issue 2005
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tagsartificial intelligence point mutation protein engineering protein sequence analysis proteins tertiary protein structure thermodynamics

ILMTool Content

http://cic.cs.wustl.edu/RNA/

RNA > Structure Prediction, Visualization, and Design

Server which provides iterated loop matching and maximum weighted matching algorithms for pseudoknot containing RNA secondary structure prediction. Algorithms can apply thermodynamic and comparative information, and thus can be used for either aligned or individual sequences.

NAR Web Server Issue 2004
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tagsalgorithms bacillus subtilis bacterial rna base composition base pairing base sequence escherichia coli feedback molecular models molecular sequence data nucleic acid conformation nucleic acid sequence homology phylogeny reproducibility of results rna rna sequence analysis sensitivity and specificity sequence alignment theoretical models thermodynamics transfer rna

MfoldTool Content

http://mfold.rna.albany.edu/?q=mfold/download-mfold

RNA > Structure Prediction, Visualization, and Design

Predict RNA secondary structure from sequence; does not predict pseudoknots - see PKNOTS.

NAR Web Server Issue 2003
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tagsbase composition base sequence consensus sequence dna molecular models molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid denaturation nucleic acid hybridization nucleic acid repetitive sequences rna single-stranded dna thermodynamics

MinActionPathTool Content

http://lorentz.immstr.pasteur.fr/joel/index.php

Protein > 3-D Structure Retrieval/Viewing
Protein > Molecular Dynamics and Docking

MinActionPath calculates the most-probable trajectory between two known structural states of a protein.

NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence biological models chemical models computational biology computer simulation energy transfer molecular models molecular sequence data protein conformation proteins tertiary protein structure theoretical models thermodynamics

ModellerTool Content

http://salilab.org/modeller/

Protein > 3-D Structure Prediction

Homology or comparative modeling of 3D protein structures.

NAR Web Server Issue 2003
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tagsamino acid sequence amino acid sequence homology animals bacterial proteins biological models carrier proteins computer simulation enzymes factual databases genetic models genome genomics humans kallikreins l-lactate dehydrogenase mathematics molecular models molecular sequence data pancreatic elastase probability protein conformation protein databases protein folding protein structural homology proteins reproducibility of results sequence alignment sequence homology systems integration tertiary protein structure theoretical models thermodynamics tissue kallikreins trichomonas vaginalis trypsin

MoViESTool Content

http://ang.cz3.nus.edu.sg/cgi-bin/prog/norm.pl

DNA > Structure and Sequence Feature Detection
Protein > Annotation and Function
Protein > Molecular Dynamics and Docking
RNA > Structure Prediction, Visualization, and Design

MoViES (Molecular Vibrations Evaluation Server) allows the computation of the vibrational and thermal fluctuations dynamics for the chemical bonds of biomolecules. The server takes as input a structure file in PDB format and returns results by email. Analysis of vibrational motions and thermal fluctuational dynamics can give insights into the functional properties of both proteins and nucleic acids.

NAR Web Server Issue 2004
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tagscomputational biology hydrogen bonding nucleic acids proteins thermodynamics vibration

NNDBDatabase Content

http://rna.urmc.rochester.edu/NNDB

DNA > Databases

The Nearest Neighbor Database (NNDB) is a web-based resource for disseminating parameter sets for predicting nucleic acid secondary structure stabilities. For each set of parameters, the database includes the set of rules with descriptive text, sequence-dependent parameters in plain text and html, literature references to experiments and usage tutorials. Also covered are parameters for predicting RNA folding free energy and enthalpy changes.

NAR Database Issue 2010
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tagsalgorithms base sequence computational biology genetic databases molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid denaturation rna thermodynamics

NQ-FlipperTool Content

https://flipper.services.came.sbg.ac.at/cgi-bin/flipper.php

Protein > 3-D Structure Prediction

NQ-Flipper recognizes unfavorable rotamers of Asn and Gln residues in protein structures.

NAR Web Server Issue 2007
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tagsamides asparagine computational biology crystallography escherichia coli glutamine molecular conformation molecular models protein conformation protein databases protein folding proteins reproducibility of results statistical data interpretation stereoisomerism structural models thermodynamics

oGNMTool Content

http://ignm.ccbb.pitt.edu/GNM_Online_Calculation.htm

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.

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

OligoArrayTool Content

http://berry.engin.umich.edu/oligoarray2_1/

Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Model Organisms > General Resources

OligoArray is free software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction. A database of pre-designed oligonucleotide microarray probes for organisms with a fully sequenced genome can be found at http://berry.engin.umich.edu/oligoarraydb/index.html

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tagsalgorithms arabidopsis gc rich sequence gene expression profiling genetic transcription nucleic acid conformation oligonucleotide array sequence analysis oligonucleotide probes plant genome thermodynamics