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Links tagged with 'water'

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Found 5 links

Displaying 5 links

3DSSTool Content

http://cluster.physics.iisc.ernet.in/3dss/options.html

Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing

3-Dimensional Structural Superposition (3DSS) is a tool for superposing two or more protein structures that uses RASMOL for visualization; some browser configuration is necessary.

NAR Web Server Issue 2006
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tagsmolecular models phospholipases a protein databases protein structural homology water

NDB ToolsTool Content

http://ndbserver.rutgers.edu/services/

RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

The Nucleic Acid Database (NDB) Tools page includes RNAView and BPView, programs for the visualization and classification of RNA base pairs, motifs, and structures.

NAR Web Server Issue 2003
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tagsalgorithms base pairing base sequence chemical models dna factual databases molecular models molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology proteins restriction mapping ribosomal rna rna signal recognition particle statistical data interpretation stereoisomerism terminology as topic water

PDB_HydroTool Content

http://lorentz.immstr.pasteur.fr/solvate_mutate.php

Protein > 3-D Structural Features
Protein > Biochemical Features

PDB_Hydro provides tools for mutating and solvating structures of biological macromolecules like proteins or DNA. It identifies strongly and poorly solvated exposed surfaces of structures in an effort to help identify potential interaction zones.

NAR Web Server Issue 2006
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tagsbinding sites dimerization lipids mathematical computing membrane proteins nucleic acids protein conformation protein databases proteins solvents static electricity water

ReadOutTool Content

http://gibk26.bio.kyutech.ac.jp/jouhou/readout/

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.

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

SPACETool Content

http://ligin.weizmann.ac.il/space/

Protein > 3-D Structure Prediction

SPACE (Structure Prediction and Analysis based on Complementarity with Environment) is a suite of tools for predicting and analyzing structures of biomolecules and their complexes.

NAR Web Server Issue 2005
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tagsalgorithms amino acids automation bacterial proteins binding sites biotin computational biology factual databases formycins hydrogen bonding ligands molecular conformation molecular models molecular structure nucleic acids point mutation protein binding protein conformation protein databases proteins ribonucleotides ricin site-directed mutagenesis solvents streptavidin thermodynamics water x-ray crystallography