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. |