Computational Framework for Biotechnological Research

Structural analysis

Structural analysis used for determination of a protein's 2D/3D structure is crucial in the study of its function.

Software Name Description
RasMol RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures, such as those found in the Protein Data Bank.
QuteMol QuteMol is an open source, interactive, molecular visualization system used for studying 3D shape and structure of large molecules or complex proteins
PyMol PyMOL is a powerful and comprehensive molecular visualization product for rendering and animating 3D molecular structures.
MeshLab MeshLab is an open source, portable, and extensible system for the processing and editing of unstructured 3D triangular meshes.
Chimera UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.
SwissPDB Viewer Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface
Molekel Molekel is a free and open-source multiplatform molecular visualization program
Cytospace Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.
BioClipse Molecular Editor
Avogadro Avogadro is a 3D molecular structure editor used for editing three-dimensional molecular compositions indicating molecule from every conceivable angle and perspective.
Jmol Jmol is an open-source Java viewer for three-dimensional chemical structures, with features for chemicals, crystals, materials and biomolecules.
Ascalaph Designer Ascalaph Designer provides the methods to build and edit molecular models, geometry optimization, molecular dynamics simulations.
GROMACS GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics simulation package designed for biomolecular systems such as proteins and lipids.
MDynaMix MDynaMix (Molecular Dynamics of Mixtures) is a general purpose molecular dynamics software package for simulations mixtures of molecules, interacting by AMBER/CHARMM like force fields in a periodic boundary conditions.
TINKER The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.
NAMD NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
DaliLite DaliLite is a program for pairwise structure comparison and for structure database searching. It is a standalone version of the search engine of the popular Dali server.
EMSearch Emsearch is a search tool for electron microscopy depositions.
MaxSprout MaxSprout is a fast database algorithm for generating protein backbone and side chain co-ordinates from a C(alpha) trace.
MSDfold MSD Fold is a secondary structure matching tool. It also compares protein chains/structures and look for similar ones in the whole PDB archive or among SCOP domains.
MSDpro MSD pro is a java applet tool that allows you to construct complex relational queries on the PDBe, without needing to know the arrangement of the data within the database, or the language in which such queries are usually written, SQL.
PDBeSite PDBeSite is a tool which allows the ability to search the active site database based on ligand (eg ATP) or active site (eg CYS CYS CYS CYS) information.
NMR Representatives NMR Representatives is a search tool for NMR elucidated structures in the PDB.
PDBE Services PDBE Services is a complete list and summary of all the tools and services the Protein Databank in Europe (PDBe) group have to offer.
PQS Parallel Quantum Solutions (PQS) provides parallel computers with integrated software for high-performance computational chemistry.
PQS - Quick PQS-Quick ia a structural analysis tool which quickly retrives protein quaternary structure information from PDB ID code.
PROCOGNATE PROCOGNATE is a database of cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam.
Tempura Tempura is a function prediction tool and local structural comparison service. It uses the "reverse template" approach published as part of the ProFunc server but has been modified to allow the user to specify the amino acids to be used in the template generation process.
PDBeFOLD PDBeFold (also known as SSM) is an interactive service for comparing protein structures in 3D. This service provides pairwise and multiple comparison and 3D alignment of protein structures, examination of a protein structure for similarity with the whole PDB archive or SCOP archive.
Receptor Binding Domain Finder The receptor binding domain finder tries to detect domains in a protein that might be involved in protein-protein interaction by analyzing the amino acid sequence only.