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Structural > Analysis & Verification

3DNA
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
ACT is a program that analyzes coordinates. It provides B-factor statistics and finds all crystal contacts.
Curves
Curves calculates a helical parameter description for any nucleic acid segment with respect to an optimal, global helical axis.
DOWSER
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.
DSSPCont
The DSSP program automates protein secondary structure assignment from PDB structures.
Dali
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.
FEATURE
WebFEATURE allows a user to scan a molecular structure for a particular functional site.
GRASP
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
HBexplore is a tool to identify and then analyze hydrogen bonds in biological macromolecules.
MIFit
MIFit was originally developed by Duncan McRee as a replacement for his popular xfit program.
MolProbity
Web service for all-atom contact and geometrical analysis of your model.
NOC
The menu-driven operation of NOC makes it easy to use and flexible environment to explore macromolecular structures.
PARVATI
PARVATI (Protein Anisotropic Refinement Validation and Analysis Tool) is a validation/analysis tool for macromolecular structure refinements that include anisotropic displacement parameters.
PISA
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.
PRIDE2
Protein fold similarity Web server
PiQSi
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
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
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
WHAT_CHECK is a downloadable structure valiadation suite based upon the DSSP and WHAT IF programs.