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amino_acids

amino_acids

 
 

benchmark

benchmark

 
 

checkpoints

checkpoints

 
 

databases

databases

 
 

designs

designs

 
 

hairpin

hairpin

 
 

lib

lib

 
 

rotamer_library

rotamer_library

 
 

test_peptides

test_peptides

 
 

tinker_jobs

tinker_jobs

 
 

.gitignore

.gitignore

 
 

AMOEBA.txt

AMOEBA.txt

 
 

AStarEnergyCalculator.java

AStarEnergyCalculator.java

 
 

AbstractTorsion.java

AbstractTorsion.java

 
 

AminoAcid.java

AminoAcid.java

 
 

Atom.java

Atom.java

 
 

BackboneFingerprint.java

BackboneFingerprint.java

 
 

BackboneMutator.java

BackboneMutator.java

 
 

BetaSheetGenerator.java

BetaSheetGenerator.java

 
 

CatalystDesigner.java

CatalystDesigner.java

 
 

CatalystRotamerSpace.java

CatalystRotamerSpace.java

 
 

Chirality.java

Chirality.java

 
 

Client.java

Client.java

 
 

DCLMAreaCalculator.java

DCLMAreaCalculator.java

 
 

DEECalculator.java

DEECalculator.java

 
 

DEEDoubles.java

DEEDoubles.java

 
 

DEESingles.java

DEESingles.java

 
 

DEEenergyCalculator.java

DEEenergyCalculator.java

 
 

DatabaseLoader.java

DatabaseLoader.java

 
 

DiscreteProbabilityDistribution.java

DiscreteProbabilityDistribution.java

 
 

Element.java

Element.java

 
 

EnergyBreakdown.java

EnergyBreakdown.java

 
 

FileFormat.java

FileFormat.java

 
 

FixedSequenceMonteCarloJob.java

FixedSequenceMonteCarloJob.java

 
 

FixedSequenceMonteCarloJobViewer.java

FixedSequenceMonteCarloJobViewer.java

 
 

FixedSequenceRotamerSpace.java

FixedSequenceRotamerSpace.java

 
 

Forcefield.java

Forcefield.java

 
 

GaussianInputFile.java

GaussianInputFile.java

 
 

GeneralThreadService.java

GeneralThreadService.java

 
 

HydrogenBondMutator.java

HydrogenBondMutator.java

 
 

Immutable.java

Immutable.java

 
 

IndexPair.java

IndexPair.java

 
 

IndexTorsion.java

IndexTorsion.java

 
 

InputFileFormat.java

InputFileFormat.java

 
 

Interaction.java

Interaction.java

 
 

Molecule.java

Molecule.java

 
 

MonteCarloJob.java

MonteCarloJob.java

 
 

MonteCarloResult.java

MonteCarloResult.java

 
 

Mutator.java

Mutator.java

 
 

NonRotamericLibrary.java

NonRotamericLibrary.java

 
 

OPLS.txt

OPLS.txt

 
 

OPLScalculator.java

OPLScalculator.java

 
 

OPLSforcefield.java

OPLSforcefield.java

 
 

OmegaDatabase.java

OmegaDatabase.java

 
 

OutputFileFormat.java

OutputFileFormat.java

 
 

Pair.java

Pair.java

 
 

Peptide.java

Peptide.java

 
 

PeptideArchive.java

PeptideArchive.java

 
 

PeptideChargeCalculator.java

PeptideChargeCalculator.java

 
 

PeptideFactory.java

PeptideFactory.java

 
 

PeptideFingerprint.java

PeptideFingerprint.java

 
 

ProtoAminoAcid.java

ProtoAminoAcid.java

 
 

ProtoAminoAcidDatabase.java

ProtoAminoAcidDatabase.java

 
 

ProtoAminoAcidFile.java

ProtoAminoAcidFile.java

 
 

ProtoTorsion.java

ProtoTorsion.java

 
 

README.md

README.md

 
 

RamachandranDatabase.java

RamachandranDatabase.java

 
 

ReferenceEnergyCalculator.java

ReferenceEnergyCalculator.java

 
 

RemoteFuture.java

RemoteFuture.java

 
 

RemoteResult.java

RemoteResult.java

 
 

RemoteWorkUnit.java

RemoteWorkUnit.java

 
 

Residue.java

Residue.java

 
 

Result.java

Result.java

 
 

Rotamer.java

Rotamer.java

 
 

RotamerDatabase.java

RotamerDatabase.java

 
 

RotamerFactory.java

RotamerFactory.java

 
 

RotamerIterator.java

RotamerIterator.java

 
 

RotamerLibrary.java

RotamerLibrary.java

 
 

RotamerMutator.java

RotamerMutator.java

 
 

RotamerPair.java

RotamerPair.java

 
 

RotamerSpace.java

RotamerSpace.java

 
 

RotamerSummarizer.java

RotamerSummarizer.java

 
 

RotamericLibrary.java

RotamericLibrary.java

 
 

Server.java

Server.java

 
 

Settings.java

Settings.java

 
 

ShrakeRupleyCalculator.java

ShrakeRupleyCalculator.java

 
 

SidechainMutator.java

SidechainMutator.java

 
 

Singleton.java

Singleton.java

 
 

Superposition.java

Superposition.java

 
 

SurfaceAreaCalculator.java

SurfaceAreaCalculator.java

 
 

TinkerAnalysisJob.java

TinkerAnalysisJob.java

 
 

TinkerAnalyzeOutputFile.java

TinkerAnalyzeOutputFile.java

 
 

TinkerJob.java

TinkerJob.java

 
 

TinkerKeyFile.java

TinkerKeyFile.java

 
 

TinkerMinimizationJob.java

TinkerMinimizationJob.java

 
 

TinkerXYZInputFile.java

TinkerXYZInputFile.java

 
 

TinkerXYZOutputFile.java

TinkerXYZOutputFile.java

 
 

VariableSequenceMonteCarloJob.java

VariableSequenceMonteCarloJob.java

 
 

VariableSequenceRotamerSpace.java

VariableSequenceRotamerSpace.java

 
 

WorkUnit.java

WorkUnit.java

 
 

Repository files navigation

MANDOR 2

This program designs beta-hairpins of 10-20 residues for the catalysis of ester hydrolysis.

Mandor is Merlin's stepbrother in Roger Zelazny's Chronicles of Amber. It is an anagram for "random"!

http://imgs.xkcd.com/comics/purity.png

January 2014: Began major refactoring.

April 2014: Program started.

Harvard University, Jacobsen Research Group Eugene Kwan Artur Meller Charles Yeung

Newcastle Greg Maloney

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protein design algorithms for peptides

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