Meiler Lab Computational Chemical and Structural Biology |
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Download the BCL | ||
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Mac OS X 10.4 - 10.14 | Linux x86_64 (64-bit) CentOS 6+ / RedHat 6+ pre-RH6 compile from source available from the license server |
Windows x86 (32-bit) |
bcl-4.3.1.dmg | bcl-4.3.1-Linux-x86_64.sh | bcl-4.3.1-Windows-x86.exe |
To run bcl applications, academic users need a license from our license server Commercial users need to contact us at bcl-commercial-support@meilerlab.org for licensing and pricing information |
BCL Applications | ||
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Group | Application Name | Description |
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 | |