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Name Description Links
a versatile, integrated software system for the analysis, rebuilding, and visualization of 3-dimensional nucleic acid structures.
a bioinformatics tool to generate customized fold libraries for fragment-based molecular replacement. It provides several algorithms to interpret and analyze protein structures.
(Adaptive Poisson-Boltzmann Solver) a software package designed for the numerical solution of the Poisson-Boltzmann equation (PBE), solves the equations of continuum electrostatics for large biomolecular assemblages.
a suite of programs that analyze the quality of biomolecular structures determined via NMR spectroscopy. AQUA was initially developed by Ton Rullmann and Jurgen Doreleijers at the Bijvoet Center for Biomolecular Research, Utrecht,
a Java application that allows you to design your RNA 2D structure interactively and to create and assemble the corresponding RNA 3D modules directly in UCSF Chimera.
an extension to Molscript that adds sticks and spheres, stereo pictures, flexible colouring (colour ramping) and map drawing.
a software tool for the analysis and visualisation of tunnels and channels in protein structures. This is the command line version, not the PyMOL plugin version.
a software tool for the calculation, analysis, and real-time visualization of access tunnels and channels in static and dynamic protein structures with an intuitive GUI.
offers a quick and easy way to create beautiful publication quality images and movies and to superpose and analyze structures.
(The Channel Annotation Package) a tool for the functional annotation of novel ion channel structures that provides information on the biophysical properties of the ion permeation pathway by utilising molecular dynamics simulations.
a highly extensible, interactive molecular graphics 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. It is often a tool of choice for rendering EM volumes.
the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. Compared to Chimera, ChimeraX has improved graphics (e.g. interactive ambient shadows); faster handling of large structures (millions of atoms); and a more modern, single-window user interface.
an interactive contact map visualization and analysis tool.
an easy-to-use Notebook based environment for fast and convenient protein structure predictions.
ligand binding site prediction from protein sequence and structure.
(Crystallographic Object-Oriented Toolkit) supports model building and real space refinement. This application interfaces with refmac, Phenix, and several other applications. Coot was recognized as the best structural biology application in 2008 by SBGrid.
an algorithm for calculating a helical parameter description for any irregular nucleic acid segment with respect to an optimal, global helical axis.
a complete rewrite of the Curves approach for analyzing the structure of nucleic acids. Included are the helper programs Canal, Cdif and Sumr.
a program for calculating protein electrostatics.

Restriction: available to nonprofit users who register with Columbia & submit confirmation to SBGrid.
a realtime 3D visualization program for structural biology data.
performs efficient geometry-based conformational sampling of protein structures under experimental restraints. It combines prior structural information with experimental data through the Deformable Elastic Network (DEN) approach which drastically reduces over-fitting.
a program that surveys a protein molecule's structure to locate internal cavities and assess hydrophilicity in terms of the energy of interaction of a water molecule with the surrounding atoms. Experience has shown that cavities with interaction energies below -12 kcal/mol tend to be filled, and cavities for which the energy is above that threshold, tend to be empty.
a program that standardizes secondary structure assignment calculated from a coordinate file. Secondary structure prediction is not supported. Designed by Wolfgang Kabsch and Chris Sander
(Dissecting the Spatial Structure of RNA) a software tool for dissecting the spatial structure of RNA.
a program to determine domains, hinge axes and hinge bending residues in proteins where two conformations are available.
a program to analyze domain movements in large, multi-chain, biomolecular complexes, useful for any molecule for which two atomic structures are available that represent a conformational change indicating a possible domain movement.
a scientific image processing suite with a particular focus on single particle reconstruction from cryoEM images. EMAN2 is a complete refactoring of the original EMAN1 library and contains the SPARX applications.
a JAVA program that reads PDB files containing a nucleic-acid protein complex and gives a listing of interactions that occur at the interface between the nucleic-acid/protein complex and classifies these interactions into hydrogen bonds, electrostatic, hydrophobic, and Van der Waals. Entangle also recognizes when a stacking interaction occurs between two aromatic residues.
a script driven program that analyzes and compares three-dimensional protein structures. The current version (0.7) is mostly designed to find the rigid part of protein molecules by comparing different structures.

Restriction: available to nonprofit users who register with EMBL & submit confirmation to SBGrid.
a tool to predict protein structure, function, and mutations using evolutionary sequence covariation.
enables fast and sensitive comparisons of large structure sets.
an open source protein pocket (cavity) detection algorithm based on Voronoi tessellation. It was developed in the C programming language and is currently available as command line driven program.
(High Ambiguity Driven biomolecular DOCKing) relies on an approach that makes use of biochemical and/or biophysical interaction data, such as chemical shift perturbation data resulting from NMR titration experiments, mutagenesis data or bioinformatic predictions.
a neural network for the automatic identification of oligonucleotides and protein secondary structure in cryo‐EM maps.
a program suite (hbplus, access and clean) to compute hydrogen positions, hydrogen bonds, and neighboring interactions. The application was developed at University College London.
an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
a program that allows the analysis and visualisation of the pore dimensions of the holes through molecular structures of ion channels.
computes the hydrodynamic properties of rigid macromolecules (proteins, small nucleic acids, macromolecular complexes, etc.) from their structure, as specified by the coordinates taken from a PDB file supplied by the user, from which the proper hydrodynamic model is built by the program itself.
a high quality visualizer and annotator for three dimensional molecular structures, sequences, alignments, chemical spreadsheets and biological data.
Illustrate is a small Fortran program for creating non-photorealistic illustrations of molecules, with cartoony colors and outlines, and soft ambient shadows. I originally developed it during postdoctoral training in the laboratory of Arthur J. Olson at the Scripps Research Institute, and have tinkered with it ever since. I have used it to create materials for my books and for PDB-101, the outreach portal of …
an efficient tool for flexible fitting of atomic structures into EM maps based on Normal Mode Analysis in internal Coordinates.
a multiple sequence alignment editor written in Java. It is used widely in a variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain database) but is available as a general purpose alignment editor.
a program for automatically plotting protein-ligand interactions.
the successor to the original LIGPLOT program for automatic generation of 2D ligand-protein interaction diagrams. It is run from an intuitive java interface which allows on-screen editing of the plots via mouse click-and-drag operations.
a program for calculating the curvature of nucleic acids. From a given list of base pair step roll, tilt and twist values, and the specification of a reference plane, the program produces the global tilt, global roll and the bend magnitude. These quantities describe the direction and magnitude of a bend angle for analysis of DNA and DNA/protein complex geometries.
a package that does multiple alignment of protein structures, providing a common 3D superimposition, a corresponding structure-based sequence alignment and a dendrogram for the set of structures aligned.
a multiple protein structure alignment program. It uses local geometry to align segments of two sets of proteins, allowing limited bends in the backbones between the segments.
an application that assists in the processing and curation of macromolecular structure data.
(Multi-Conformation Continuum Electrostatics) a biophysics simulation program combining continuum electrostatics and molecular mechanics. In this program, the protein side chain motions are simulated explicitly while the dielectric effect of solvent and bulk protein material is modeled by continuum electrostatics.
a program that is used for including solvation effects in biological systems, such as proteins, using an atomic model of the protein. This is done by solving the Poisson-Boltzmann equation in a dielectric medium, including distributed point charges on a grid.
a software package for visualization and analysis of molecular structures comprising AutoDockTools (ADT): a graphical front-end for setting up and running AutoDock; Python Molecule Viewer (PMV); and Vision: a visual-programming environment for building networks describing novel combinations of computational methods and yielding new visualizations of their data.
an interactive graphics application for molecular modeling, fitting, and refinement of protein structures from X-ray crystallography developed by Bradley Smith as an Open Source project while working for Rigaku/MSC Inc. A particular focus of the MIFit software is the efficient solution and analysis of protein:ligand complexes.
is a program for comparative modeling of RNA 3D structures.
a universal toolkit rapid, automated location and characterization of channels and pores in molecular structures. The core of the MOLE algorithm is a Dijsktra path search algorithm, which is applied to a Voronoi mesh. It can explore large molecular channels, complex networks of channels, and molecular dynamics trajectories that requires analysis of a large number of snapshots.
a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules.
a protein structure analysis platform offering quality validation for 3D structures of proteins, nucleic acids and complexes.
a program for creating schematic or detailed, publication-quality molecular graphics images from molecular 3D coordinates, usually, but not exclusively, protein structures.
a stand-alone program that calculates the accessible area of a molecule from a PDB format file.
a Perl program that allows PyMOL to display atomic models of nucleic acids in a highly simplified representation.
a program to generate schematic diagrams of protein-DNA interactions. The program works for any single- or double-stranded protein-DNA, DNA-ligand and protein-RNA complexes.
a model building application for X-ray crystallography.
a trainable, memory-efficient, and GPU-friendly PyTorch reproduction of DeepMind's AlphaFold 2.
a high performance toolkit for molecular simulation that can be used either as a stand-alone application for running simulations or as a library you call from your own code.
identifies and assigns carbohydrate structures using only atom types and their 3D atom coordinates given in PDB-files. Looking up a translation table where systematic names and the respective PDB residue codes are listed, both assignments are compared and inconsistencies are reported.
a C/C++ application developed as a coordinate and protein NMR restraint converter. This user-friendly tool provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, and analysis of atomic position consistency based on their convergence across a protein NMR ensemble.
a set of tools used by the PDB for processing and checking structure data.
an application to evaluate atomic packing, either within or between molecules. It generates “contact dots” where atoms are in close contact. Probe reads atomic coordinates from protein databank (PDB) format files and writes dot-lists for inclusion in a kinemage file.
a program for checking the stereochemical quality of a protein structure, producing a number of PostScript plots analyzing its overall and residue-by-residue geometry.
the ultimate protein least squares fitting program.
(PROfile Multiple Alignment with predicted Local Structure) a progressive method for aligning multiple protein sequences, with enhanced profile information from database searches and secondary structure prediction.
predicts the pKa values of ionizable groups in proteins (version 3.0) and protein-ligand complexes (version 3.1 and later) based on the 3D structure.
converts a protein sequence alignment in BLAST, CLUSTAL or MSF format to a property file used to map the sequence conservation onto the structure of a protein using the GRASP program or the MOLMOL program or the PyMOL program. A pseudo-PDB file with the sequence conservation score in place of the temperature factor is also provided, to use with programs such as InsightII (accelrys).
widely used molecular visualization package developed by Warren DeLano, now maintained by Schödinger, LLC. This installation includes official incentive builds of PyMOL.

Restriction: available to non-profit groups in North America, Europe, Asia, and Australia.
a "quick" evaluation of steric packing in protein structures. Amino acid side chains are not represented in full atomic detail, but instead uses one or more averaged centers of interaction per residue. Side chain packing quality is determined from the spherical space available to each residue. Empirical pairwise residue contact potential can be used to estimate the correctness of model protein structures.
detects contiguous stretches of hydrophobic surface area on the surfaces of macromolecules.
a comprehensive, platform-independent, user-friendly, and complete software package that enables efficient, reliable, highly automated, and accurate analysis of high-throughput capillary electrophoresis-detected nucleic acid chemical probing experiments.
a program to assist in aesthetic drawings of RNA secondary structures. It is primarily aimed at drawing consensus diagrams, but can also draw single RNA molecules.
a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.
a set of tools for generating high quality raster images of proteins or other molecules.
a collection of cheminformatics and machine-learning software written in C++ and Python.
(Resolution Map) a Python (NumPy/SciPy) application with a Tkinter GUI. It is an easy to use software package for computing the local resolution of 3D density maps studied in structural biology, primarily electron cryo-microscopy (cryo-EM). ResMap has a both a GUI (window) and a command line interface.
protein hallucination and inpainting with RoseTTAFold.
a modular toolkit developed to deal with RNA structure probing and post-transcriptional modifications mapping high-throughput data. Toolkit will help with automatic reference transcriptome creation, automatic reads preprocessing (adapter clipping and trimming) and mapping, scoring and data normalization, and accurate RNA folding prediction by incorporating structural probing data.
a visualization tool that displays/edits 2-dimensional diagrams of RNA/DNA secondary structures with tertiary interactions created by RNAView. It generates standard molecular representations (e.g. tRNA cloverleaf structures) or any structural representations by rearranging various parts (e.g helices and single strands) of the RNAView 2D diagrams. RNA motifs are rapidly identified and classified with the base pair annotation and the 2D graphic display.
a complete package for RNA and DNA secondary structure prediction and analysis.
quickly displays the secondary structure of RNA/DNA with tertiary interactions. It is fully implemented with Leontis and Westhof's ( RNA (2001) 7, 499-512), convention for the edge-to-edge hydrogen bonding interactions.
an interactive multi-resolution docking and visualization program for low-resolution density maps and atomic structures.
a completely rewritten version of our ShapeMapper for reading out the results of an RNA chemical probing experiment by massively parallel sequencing that integrates careful handling of all classes of adduct-induced sequence changes, sequence variant correction, basecall quality filters, and quality-control warnings to identify RNA adduct sites.
is a program that generates publication-quality protein secondary structure diagrams from three-dimensional protein structures. To depict relationships between secondary structure and other protein features, diagrams can be colored by conservation score, B-factor, or custom scoring.
(STructural Alignment of Multiple Proteins) a suite of programs to compare and align protein 3-D structures. It will multiply align structures and produce a corresponding sequence alignment with confidence values associated with each aligned position. It will also search a database of protein structures to identify structurally similar proteins and includes a number of utility programs for the manipulation of protein structures.
a program to recognize secondary structural elements in proteins from their atomic coordinates.
a pipeline that uses data obtained from ShapeMapper to model RNA secondary structures, including pseudoknots; identify de novo regions with well-defined and stable structures; and visualize most probable and alternative helices.
calculates exact accessible surface area, molecular surface area and average curvature of molecular surface for macromolecules. The program also analyzes cavities in the protein interior inaccessible to solvent from outside.
a program that generates surfaces, density contours and gap regions from coordinate data supplied in a PDB file.
calculates solvent accessible area that is defined by a probe as it rolls on the surface of the molecule. Thus use of a zero radius probe will give the Van der Walls surface area.
an application that provides a user friendly interface allowing you to analyze several proteins at the same time.
a program for the simultaneous superpositioning and analysis of multiple macromolecular structures via the method of maximum likelihood (ML).
the Swiss Army knife of crystallography tools. The installation includes the packages from RAVE, SBIN, X-UTIL, VOIDOO, DEJAVU and SPASM. And includes the following binaries: * aconio * cello * comap * crave * essens * flood * lsqman * mama.debug * mapman * mave * moleman2 * o2d * oops * prof * site2rt * solex * ssencs * xpand
a visual environment developed to fit interactively atomic models into 3D reconstructions. Calculations are performed in reciprocal-space and the symmetry of the reconstruction is taken into account. The computations are fast and an entire EM reconstruction can be used.
a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
a combination of the X-PLOR structure determination program and VMD (Visual Molecular Dynamics) - a freely available molecular visualization program. This package allows manual manipulation of the protein structures to satisfy experimental NMR data, and can also be used to visualize the goodness of fit of a particular model to given restraints.

Restriction: available to users who register with the NIH & submit confirmation to SBGrid.
a tool for analysis of atomic neighborhoods in molecular structures using a Voronoi diagram of balls determined from the atomic model. It is especially suitable for processing three-dimensional structures of biological macromolecules such as proteins and RNA.
searches PDB files for misidentified water molecules that should be modeled as cations.
the protein verification tool from the WHAT IF program available as a free stand-alone program, complete with all source code.
a general protein analysis program.
uses interactive computer graphics to introduce basic concepts of X-ray diffraction by crystals, including the reciprocal lattice, the Ewald sphere construction, Laue cones, the wavelength dependence of the reciprocal lattice, primitive and centered lattices and systematic extinctions, rotation photography, Laue photography, space group determination and Laue group symmetry, and the alignment of crystals by examination of reciprocal space.
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