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Structural > Analysis & Verification

3DNA calculates a complete set of local base-pair, step, and helical parameters, and allows for exact rebuilding of a structure based on these parameters.
ACT is a program that analyzes coordinates. It provides B-factor statistics and finds all crystal contacts.
Curves calculates a helical parameter description for any nucleic acid segment with respect to an optimal, global helical axis.
The Dowser program surveys a protein molecule's structure to locate internal cavities and assess the hydrophilicity of these cavities in terms of the energy of interaction of a water molecule with the surrounding atoms.
The DSSP program automates protein secondary structure assignment from PDB structures.
The Dali server compares protein structures in 3D.
ERRAT Structure Verification Server
ERRAT is a protein structure verification algorithm that works by analyzing the statistics of non-bonded interactions between different atom types.
Electron Density Server
The Uppsala Electron Density Server can be used to readily obtain electron density maps of deposited structures.
WebFEATURE allows a user to scan a molecular structure for a particular functional site.
GRASP is a molecular visualization and analysis program. It is particularly useful for the display and manipulation of the surfaces of molecules and their electrostatic properties.
HBexplore is a tool to identify and then analyze hydrogen bonds in biological macromolecules.
MIFit was originally developed by Duncan McRee as a replacement for his popular xfit program.
Web service for all-atom contact and geometrical analysis of your model.
The menu-driven operation of NOC makes it easy to use and flexible environment to explore macromolecular structures.
PARVATI (Protein Anisotropic Refinement Validation and Analysis Tool) is a validation/analysis tool for macromolecular structure refinements that include anisotropic displacement parameters.
PISA (Protein Interfaces, Surfaces and Assemblies) is an interactive tool for the exploration of macromolecular (protein, DNA/RNA and ligand) interfaces, prediction of probable quaternary structures (assemblies), database searches of structurally similar interfaces and assemblies, as well as searches on various assembly and PDB entry parameters.
Protein fold similarity Web server
PiQSi is a community effort that facilitates the investigation and curation of quaternary structures.
STING Millennium
STING Millennium is a web based suite of programs that starts with visualizing molecular structure and then leads a user through a series of operations resulting in a comprehensive structure analysis.
Symmetry Equivalent Molecules
A web based GUI to generate and visualize the macromolecules.
VMD (Visual Molecular Dynamics) is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
Verify3D Structure Evaluation Server
Verify3D (UCLA-DOE) server is a tool designed to help in the refinement of crystallographic structures.
WHAT IF is a versatile molecular modeling package that is specialized on working with proteins and the molecules in their environment like water, ligands, nucleic acids, etc.
WHAT_CHECK is a downloadable structure valiadation suite based upon the DSSP and WHAT IF programs.