AutoAssign is a constraint-based expert system for automating the analysis of backbone resonance assignments using NMR spectra of small proteins.

AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. Search methods include evolutionary methods such as the Lamarckian Genetic Algorithm, in addition to the Monte Carlo simulated annealing (SA) method.

Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers a flexible rendering engine and a powerful plugin architecture.

B-BOP (Block Bond-Order Potential method) is a program for performing O(N) tight-binding (TB) calculations of molecules and bulks, based on block bond-order potential method within semi-empirical TB models. Molecular dynamics (MD) simulations for the NEV ensemble and the geometry optimization by the steepest decent (SD) method can be performed.

Babel is a program designed to interconvert a number of file formats used in molecular modeling. Babel is capable of assigning hybridization, bond order, and connectivity when these elements are not present in the input file.

BallView is a cross-platform molecular visualization tool with support for molecular mechanics optimisation, molecular dynamics and molecular editing. It supports a large number of file formats, SMILES and SMARTS, as well as forcefields such as Amber, MMFF94 and Charmm. Its capabilities also include realtime raytracing and stereoscopic viewing. Actions can be automated using Python scripts.

BIGMAC stands for Beyond Impressive Goals of Mechanical Artificial Computations. It uses Configurational Bias Monte Carlo (CBMC) to compute thermodynamic properties of flexible molecules. It has been used to study the adsorption behavior of linear and branched alkanes in zeolites and the vapour-liquid equilibrium of linear and branched alkanes.

Bioclipse is a Java-based visual platform for chemo- and bioinformatics with a plugin architecture that currently includes plugins for the CDK and Jmol.

Bist (Bidimensional Structures) is a chemical drawing program focussed on organic chemistry. Using the OpenBabel API, it can import/export in a wide variety of file formats including CML. A notable feature is that it can automatically parse linear fragments to create a 2D structure.

BKChem is a chemical drawing program written in Python. One of its notable features is SVG export.