Structural Biology Software Database
Structural Biology Software Database

Application Index

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Category: Molecular Building (18 entries)

Applications for constructing molecules (or system of molecules) from small organic/inorganic molecules to macromolecules like proteins DNA/RNA and polymers.


3DNA is a versatile package for analyzing and rebuilding 3-dimensional nucleic acid structures. It is available on SGI and Linux platforms.
View Application Entry for 3DNA


ChemEdit is a molecular viewer/editor for chemists as well as a general object-oriented drawing program, which runs on Silicon Graphics workstations running on IRIX 4.0.5 or later. ChemEdit is designed mainly to help scientists in the task of drawing and designing chemical structures. In addition, it offers a variety of other useful features such as drawing of common geometrical objects, formatting of text, and interactive display of molecular orbitals and electron densities. It provides graphical interfaces for the PSI88 molecular orbital plotting package and BOSS and MCPRO. The major policy behind this program is that one should be able to obtain a hard copy (PostScript output) which is as close as possible to the displayed screen. ChemEdit for SGI/IRIX is no longer being developed. If you have been a ChemEdit user, please switch to XChemEdit which is an X11/Motif version of ChemEdit.
View Application Entry for ChemEdit


Consolv is a software which predicts whether water molecules bound to the surface of a protein are likely to be conserved or displaced in other, independently-solve crystallographic structures of the same protein.
View Application Entry for Consolv


Dowser program surveys the structure of a protein molecule 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. Experience has shown that cavities with interaction energies below -12 kcal/mol tend to be filled, and cavities for which the energy is greater than that threshold, tend to be empty.
View Application Entry for Dowser

EGAD: protein design and mutant stability and affinity prediction

EGAD is a free, open-source software package for protein design and prediction of mutation effects on protein folding stabilities and binding affinities to 1kcal/mol. EGAD can also consider multiple structures simultaneously for designing specific binding proteins or locking proteins into specific conformational states. In addition to natural protein residues, EGAD can also consider free-moving ligands with or without rotatable bonds. EGAD can be used with single or multple processors.
View Application Entry for EGAD: protein design and mutant stability and affinity prediction


Gabedit is a graphical user interface to computational chemistry packages like Gamess-US, Gaussian, Molcas, Molpro, MPQC PCGamess and Q-Chem. It can display a variety of calculation results including support for most major molecular file formats. The advanced "Molecule Builder" allows to rapidly sketch in molecules and examine them in 3D. Graphics can be exported to various formats, including animations.
View Application Entry for Gabedit

HIC-Up (Hetero-compound Information Centre - Uppsala)

HIC-Up (The Hetero-compound Information Centre - Uppsala) is a freely accessible resource for structural biologists who are dealing with hetero-compounds (small molecules).
View Application Entry for HIC-Up (Hetero-compound Information Centre - Uppsala)


ISIS/Draw is a chemically intelligent drawing package that enables you to draw chemical structures using the same intuitive signs and symbols used for paper sketches. It can be installed on Windows 95/98/NT 4.0 or Power Macintosh comuters.
View Application Entry for ISIS/Draw

NAB (Nucleic Acid Builder)

NAB is a high-level language that facilitates manipulations of macromolecules and their fragments. nab uses a C-like syntax for variables, expressions and control structures (if, for, while) and has extensions for operating on molecules (new types and a large number of builtins for providing the necessary operations). We expect nab to be useful in model building and coordinate manipulation of proteins and nucleic acids, ranging in size from fairly small systems to the largest systems for which an atomic level of description makes good computational sense. As a programming language, it is not a solution or program in itself, but rather provides an environment that eases many of the bookkeeping tasks involved in writing programs that manipulate three-dimensional structural models.
View Application Entry for NAB (Nucleic Acid Builder)

NAMOT (Nucleic Acid MOdeling Tool)

Nucleic Acid MOdeling Tool(NAMOT) is a graphic tool to build and manipulate nucleic acid structures. It is built upon the reduced set of coordinates developed here at Los Alamos National Laboratory in collaboration with scientists at the Max-Planck-Institute for Biophysical Chemistry in Goettingen,Germany. Use of these reduced coordinates provide a powerful and intuitive interface to nucleic acid structure. NAMOT2 features a set of user modifiable libraries that provide flexibility for users to expand NAMOT2 to fit their research needs. The graphic user interface attempts to make the program as efficient as possible while still retaining the power of the parameter set. Both Motif and XView interfaces exist, allowing NAMOT to run on most UNIX workstations. NAMOT produces graphic output in PS and PPM formats. PDB, AMBER, and parameter formats can be used as both input and output.
View Application Entry for NAMOT (Nucleic Acid MOdeling Tool)


Simulaid can perform many Confersion, Analysis and General operations such as - Find optimal centering of a solute (finds the center of the smallest enclosing sphere of the solute) - Find optimal orientation of a solute in a cube or a rectangle (finds the orientation that results in the smallest enclosing cube or rectangle of the solute). Useful, e.g., for setting up Delphi or GCMC calculations, resp. - Optimize orientation of a solute in a periodic box to maximize the smallest image-image distance. - Convert a structure among Charmm .CRD, Brookhaven PDB, Charmm PDB (different segid location), Insight .car, Macromodel/Xcluster .dat, as well as some Insight free formats. - Make atomnames conform to Brookhaven conventions (e.g., HH12 -> 2HH1) - Convert atom and residue names among Charmm, Amber, Moil, ChemX, and PDB conventions. - Generate a list of hydrogen bonds - Generate a list of functional groups - Generate a list of 1-4 distances and torsion angles
View Application Entry for Simulaid


This program places the required number of sodium ions around a system of electric charges, e.g., the atoms of a biological macromolecule (protein, DNA, protein/DNA complex). The ions are placed in the nodes of a cubic grid, in which the electrostatic energy achieves the smallest values. The energy is re-computed after placement of each ion. A simple Coulombic formula is used for the energy: Energy(R) = Sum(i_atoms,ions) Q_i / |R-R_i| All the constants are dropped out from this formula, resulting in some weird energy units; that does not matter for the purpose of energy comparison. To speed the program up, the atoms of the macromolecule are re-located to the grid nodes, closest to their original locations. The resulting error is believed to be minor, compared to that resulting from the one-by-one ions placement, or from using the simplified energy function. The coordinates of the placed ions are printed out in the PDB format for further usage. It is recommended that the placed ions are equilibrated in a separate Monte Carlo or Molecular Dynamics simulation. Trivial modifications to the program should allow the placement of any combination of multivalent ions of different charges.
View Application Entry for Sodium


SOLVATE is a program to construct an atomic solvent environment model for a given atomic macromolecule model (solute) for use in molecular dynamics simulations.
View Application Entry for SOLVATE


SWISS-MODEL is an Automated Protein Modelling Server running at the GlaxoWellcome Experimental Research in Geneva, Switzerland. The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists World Wide.
View Application Entry for SWISS-MODEL


Wat2ions is complementary to DelPhi, the renowned solver of the Poisson-Boltzmann equation ( The electrostatic potential map, pre-computed by DelPhi, is used to replace a certain number of water molecules of the bath, surrounding a solvated macromolecule, with ions. The potential on the oxygens of the water molecules is estimated using a 3D cubic spline interpolation of the pre-computed potential. The waters with the largest potential are replaced with chlorides, and the waters with the smallest potential, with sodii. No two ions are placed closer than a certain distance to each other. To avoid placing ions too close to the macromolecule, the potential map should be pre-computed taking into account the ion-free Stern layer around the macromolecule (see DelPhi manual for further details). The coordinates of the macromolecule, the water bath (except the replaced waters), and the placed ions are output to a new PDB file.
View Application Entry for Wat2ions


WatCh tool for identifying conserved water sites and analyzing their degree of conservation using heirarchical cluster analysis of superimposed related Protein Data Bank structures.
View Application Entry for Watch

WebLab ViewerPro

WebLab ViewerPro combines state of the art molecular graphics with a full range of Windows desktop integration tools. Using the ViewerPro, you can easily visualize and share molecular information, build molecular models, and analyze organic and inorganic structures, proteins, DNA/RNA, and crystals. It is available for Windows 95/98/2000/NT or Power Macintosh computers.
View Application Entry for WebLab ViewerPro


XChemEdit is a package of programs which can 1) draw and edit three-dimensional chemical structures, 2) serve as a graphical interface to the GAUSSIAN, JAGUAR, MOPAC, and BOSS/MCPRO programs, 3) display molecular orbials, electron densities, and electrostatic potentials, 4) animate normal mode vibrations, 5) compute solvent-accessible surface area and volume and thermochemical properties, 6) and manipulate a vriety of common document formats such as Encapsulated PostScript (EPS) and FrameMaker. XChemEdit is written for X-Windows/Motif under the UNIX operating system and is known to run on SGI/IRIX, IBM RS6000/AIX, and PC/Linux system.
View Application Entry for XChemEdit

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