Download the BCL
Windows x86 (32-bit) Linux x86_64 (64-bit)
CentOS 6+ / RedHat 6+
pre-RH6 compile from source
available from the license server
Mac OS X 10.4 or greater
bcl-3.5.0-Windows-x86.exe bcl-3.5.0.dmg
To run bcl applications, academic users need a license from our license server
Commercial users need to contact us at for licensing and pricing information

BCL Applications
bcl Group of applications that use only BCL-generated input.
Cluster Hierarchical agglomerative clustering of data
protein Group of applications that primarily use or create proteins (usually PDB files).
Compare calculates the structural differences between protein models using methods such as RMSD and GDT
CreateSSEPool Generates a pool of secondary structure elements (SSEs) used by other potein applications including Fold
Fold de-novo protein structure prediction algorithm that assembles a pool of secondary structure elements. Allows for usage of experimental restraints. Formerly known as EMFold
FusionProtein designs chimeric proteins from a scaffold by fusing mutliple donor protein fragments
PDBConvert Converts PDBs to/from FASTAs and performs various deterministic manipulations of PDBs
Score Scores proteins/PDBs according to BCL energy functions
sequence Group of applications that primarily use AA sequences (usually FASTA files).
Alignment Sequence alignment with choice of alignment algorithm, scores and weights
molecule Group of applications that primarily use or create molecules (usually SDF files).
BuildFragmentLibrary BuildFragmentLibrary does what it suggests
BuildRotamerLibrary BuildRotamerLibrary does what it does
Compare compare molecules by spatial, property, fingerprint, or substructural features
ConformerGenerator Conformer generator generates small molecule conformations for ensemble of molecules that are provided
Filter MoleculeFilter filters an ensemble of molecules by a user defined criteria
GenerateHierarchicalTree CreateRotamerLibraryTreeFormat creates a hierarchical tree for an ensemble of molecules where parent nodeis immediate substructure of child node
Properties Works with string and numeric descriptions of molecules
Unique MoleculeUnique removes duplicate molecules at constitution, configuration or conformation levels, defined by user
descriptor Group of applications that primarily use or create descriptor objects.
Analyze Analyze the tanimoto overlap between descriptor sets. Formerly known as AnalyzeCodeObjectFile
GenerateDataset Generates bin files (fast, small, easier to use with other applications), csv files (human readable), or .arff files (for use with WEKA) from any combination of dataset sources.Can compute dataset statistics and compare bin files. Formerly known as GenerateDataset
RefineByScore Create a new descriptor file using the best descriptors by score. Formerly known as RefineDescriptors
ScoreDataset Scores feature columns using various criteria. Used during descriptor development and selection. Formerly known as ScoreFeatureResultDataset
SequentialFeatureSelection takes a descriptor groups file and generates new groups of features to test, based on the best descriptor set in a prior round. Formerly known as TrainModelDescriptorSelection
model Group of applications that primarily use or create machine learning models.
ComputeStatistics Evaluate quality measures of qsar model preditions or just experimental/predicted values and present resultsin table and as gnuplot graphics. Formerly known as ComputeJuryStatistics
PredictionMerge Merge cross-validation/prediction matrices horizontally or simply append. Formerly known as TrainModelPredictionMerge
Train Train any machine learning model, including ANNs, SVMs, and many more. Formerly known as TrainModel
bioinfo Group of applications that primarily use AA sequences and machine learning models.
ContactPrediction Prediction of amino acid contacts for a given sequence
Jufo predicts secondary structure for a given protein primary sequence
restraint Group of applications that primarily use or create restraints that guide protein folding.
Pofr Compute pairwise distance histogram of bcl_model and scale to experimental data. Formerly known as RestraintPofr
Saxs Create SAXS profiles from input pdb file and compare the profile generated with an experimental profile. Formerly known as SimulateSaxsData
SaxsPrep Add Simulated error and produce clean saxs signal via shannon sampling. Formerly known as SimulateSaxsDataPrep
density Group of applications that primarily use or create density maps from sequence or protein models.
FitInDensity fits atomic protein structure into cryoEM or other medium resolution (5-20 A) density maps
FitInDensityMinimize Protein model refinement using a density map. Optimizes the correlation between the given experimental density and the simulated density

BCL applications are run using the following syntax:
<group name>:<application name>
bcl.exe protein:Fold -help

  To learn more about an application, type: bcl.exe <group name>:<application name> -readme

  To learn about the options (flags/parameters) for e.g. Jufo, type: bcl.exe bioinfo:Jufo -help