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Tools

Bioinformatics tools and scientific calculators.

ABCDEFGHILMNOPQRSTUV

A

  • AbLang/app/ablang
  • AbLang-2/app/ablang-2
  • ABodyBuilder3/app/abodybuilder3
  • ADMET-AI/app/admet-ai
  • Admetica/app/admetica
  • AF-Cluster/app/af-cluster
  • AF2BIND/app/af2bind
  • AF2Dock/app/af2dock
  • Aggrescan3D/app/aggrescan3d
  • AIMNet2/app/aimnet2
  • Aliphatic Index/app/aliphatic-index
  • AllMetal3D/app/allmetal3d
  • AlphaFlow/app/alphaflow
  • AlphaFold Database Download/app/alphafold-database-download
  • AlphaFold2/app/alphafold-2
  • AlphaGenome/app/alphagenome
  • Amino acid composition/app/amino-acid-composition
  • ANARCI/app/anarci
  • ANARCII/app/anarcii
  • AntiFold/app/antifold
  • AutoDock Vina/app/autodock-vina
  • AutoDock-GPU/app/autodock-gpu

B

  • BindCraft/app/bindcraft
  • BindingDB Download/app/bindingdb-download
  • Bioinformatics tools/app/tools
  • BioPhi/app/biophi
  • Boltz-2/app/boltz-2
  • BoltzGen/app/boltzgen
  • Brenk filter/app/brenk-filter

C

  • CANYA/app/canya
  • Carbon/app/carbon
  • Chai-1/app/chai-1
  • ChEBI Download/app/chebi-download
  • ChEMBL Download/app/chembl-download
  • Chou-Fasman/app/chou-fasman
  • CleaveNet/app/cleavenet
  • Clustal Omega/app/clustal-omega
  • ColabDock/app/colabdock
  • CoSiNE/app/cosine
  • CpG Island Finder/app/cpg-island-finder
  • CSV to FASTA/app/csv-to-fasta

D

  • DeepEMhancer/app/deepemhancer
  • DeepImmuno/app/deepimmuno
  • DeepSP/app/deepsp
  • DeepViscosity/app/deepviscosity
  • DFMDock/app/dfmdock
  • DiffAb/app/diffab
  • DiffDock-L/app/diff-dock
  • DLKcat/app/dlkcat
  • DNA ligation calculator/app/ligation-calculator
  • DNA mutation generator/app/dna-mutator
  • DNA Shuffle/app/dna-shuffle
  • DNA to Protein Converter/app/dna-to-protein
  • DNA to RNA converter/app/dna-to-rna
  • DNAGenIQ - Random DNA sequence generator/app/random-dna
  • DockQ/app/dockq
  • DR-BERT/app/dr-bert
  • DSSP/app/dssp
  • DynamicBind/app/dynamic-bind

E

  • EquiDock/app/equidock
  • ESM-2/app/esm-2
  • ESM-C/app/esm-c
  • ESM-IF1/app/esm-if1
  • ESMfold/app/esmfold
  • ESMFold2/app/esmfold-2
  • eToxPred/app/etoxpred
  • EvoDiff/app/evodiff
  • EvoIF/app/evoif
  • EvoPro/app/evopro
  • Extinction coefficient calculator/app/extinction-coefficient

F

  • FASTA splitter/app/fasta-splitter
  • FASTA to FASTQ Converter/app/fasta-to-fastq
  • FASTQ to FASTA converter/app/fastq-to-fasta
  • FastTree/app/fasttree
  • Filter DNA/app/filter-dna
  • Filter protein/app/filter-protein
  • FindPept/app/find-pept
  • FlowDock/app/flowdock
  • FoldSeek/app/foldseek
  • fpocket/app/fpocket

G

  • GC content calculator/app/gc-content
  • GenBank Feature Extractor/app/genbank-feature-extractor
  • GenBank to FASTA Converter/app/genbank-to-fasta
  • Genie 3/app/genie-3
  • GenMol/app/genmol
  • GeoDock/app/geodock
  • Glycosylation site finder/app/glycosylation-sites
  • gmx_MMPBSA/app/gmx-mmpbsa
  • GNINA/app/gnina
  • GRAVY/app/gravy
  • GROMACS/app/gromacs

H

  • HADDOCK3/app/haddock3
  • HighFold/app/highfold
  • HMMER/app/hmmer
  • Humatch/app/humatch
  • Hydropathy plot/app/hydropathy-plot
  • Hydrophobicity plot/app/hydrophobicity-plot
  • HyperMPNN/app/hypermpnn

I

  • IgBLAST/app/igblast
  • IgDesign/app/igdesign
  • IgGM/app/iggm
  • ImmuneBuilder/app/immunebuilder
  • InChI to SMILES/app/inchi-to-smiles
  • Instability Index/app/instability-index
  • IntelliFold 2/app/intellifold-2
  • InterPro Download/app/interpro-download
  • IPC 2.0 (isoelectric point calculator)/app/isoelectric-point-calculator
  • IPSAE/app/ipsae
  • IQ-TREE/app/iq-tree

L

  • Lead-likeness filter/app/lead-likeness-filter
  • Ligand fixer/app/ligand-fixer
  • LigandMPNN/app/ligand-mpnn
  • LightDock/app/lightdock
  • Lipinski's rule of 5/app/lipinskis-rule-of-5
  • LMI4Boltz/app/lmi4boltz
  • LocScale/app/locscale

M

  • MAFFT/app/mafft
  • mBER/app/mber
  • MD Trajectory Analysis/app/md-trajectory-analysis
  • MDGen/app/mdgen
  • MiniFold/app/minifold
  • MMseqs2/app/mmseqs2
  • MOL to SMILES/app/mol-to-smiles
  • MOL2 to SMILES/app/mol2-to-smiles
  • Molecular descriptors/app/molecular-descriptors
  • MolProbity/app/molprobity
  • MUMmer4/app/mummer4
  • MUSCLE5/app/muscle5

N

  • NetSolP-1.0/app/netsolp-1-0

O

  • ODesign/app/odesign
  • Oligo analyzer/app/oligo-analyzer
  • One-to-Three Converter/app/one-to-three
  • Open Babel/app/open-babel
  • OpenFE/app/openfe
  • OpenFold-3/app/openfold-3
  • OpenMM/app/openmm
  • ORB v3/app/orb-v3
  • ORF Finder/app/orf-finder

P

  • PAINS filter/app/pains-filter
  • PandaDock/app/pandadock
  • ParaSurf/app/parasurf
  • PDB Download/app/pdb-download
  • PDB to CIF Converter/app/pdb-to-cif
  • PDB to FASTA converter/app/pdb-to-fasta
  • PDB to MOL2 Converter/app/pdb-to-mol2
  • PDB to SDF Converter/app/pdb-to-sdf
  • PDB2PQR/app/pdb2pqr
  • PDBe Download/app/pdbe-download
  • PDBFixer/app/pdb-fixer
  • PDBsum/app/pdbsum
  • PepMimic/app/pep-mimic
  • PepMLM/app/pepmlm
  • Peptide cutter/app/peptide-cutter
  • Peptide mass calculator/app/peptide-mass
  • PeptideBuilder/app/peptidebuilder
  • pI Calculator/app/pi-calculator
  • PLIP/app/plip
  • PocketFlow/app/pocketflow
  • PocketXMol/app/pocketxmol
  • PolyXpert/app/polyxpert
  • PoseBusters/app/posebusters
  • PPAP/app/ppap
  • Primer3/app/primer3
  • ProFam/app/profam
  • ProGen2/app/progen
  • ProLIF/app/prolif
  • PROPKA 3/app/propka
  • ProstT5/app/prostt5
  • Prot2Prop/app/prot2prop
  • Protein charge plot/app/charge-plot
  • Protein molecular weight calculator/app/molecular-weight
  • Protein motif scanner/app/motif-scanner
  • Protein parameters/app/protein-parameters
  • Protein scale profiler/app/protein-scale
  • Protein stability prediction/app/protein-stability
  • Protein to DNA converter/app/protein-to-dna
  • Protein-Sol/app/protein-sol
  • Proteina-Complexa/app/proteina-complexa
  • ProteinMPNN/app/protein-mpnn
  • Protenix v2/app/protenix
  • Proteo-R1/app/proteo-r1
  • ProtGenIQ - Random protein sequence generator/app/random-protein
  • PubChem Download/app/pubchem-download
  • pyRMSD/app/pyrmsd
  • pySCA/app/pysca

Q

  • QEPPI/app/qeppi
  • QuickGO Download/app/quickgo-download

R

  • Radius of gyration/app/radius-of-gyration
  • Ramachandran plot/app/ramachandran-plot
  • RAxML-NG/app/raxml-ng
  • Reverse complement generator/app/reverse-complement
  • RFantibody/app/rfantibody
  • RFdiffusion/app/rfdiffusion
  • RFdiffusion 2/app/rfdiffusion-2
  • RFdiffusion3/app/rfdiffusion3
  • Rhea Download/app/rhea-download
  • RMSD calculator/app/rmsd-calculator
  • RNA to DNA converter/app/rna-to-dna
  • RNAalifold/app/rnaalifold
  • RNAcofold/app/rnacofold
  • RNAdistance/app/rnadistance
  • RNAdos/app/rnados
  • RNAduplex/app/rnaduplex
  • RNAeval/app/rnaeval
  • RNAfold/app/rnafold
  • RNAGenIQ - Random RNA sequence generator/app/random-rna
  • RNAinverse/app/rnainverse
  • RNALfold/app/rnalfold
  • RNAplex/app/rnaplex
  • RNAplfold/app/rnaplfold
  • RNAplot/app/rnaplot
  • RNAsubopt/app/rnasubopt
  • RNAup/app/rnaup
  • RosettaFold3/app/rosettafold3

S

  • Salmon/app/salmon
  • SASA calculator/app/sasa-calculator
  • ScanNet/app/scannet
  • SDF to PDB Converter/app/sdf-to-pdb
  • SDF to PDBQT Converter/app/sdf-to-pdbqt
  • SDF to SMILES/app/sdf-to-smiles
  • SigmaDock/app/sigmadock
  • SMILES to InChI/app/smiles-to-inchi
  • SMILES to MOL2/app/smiles-to-mol2
  • SMILES to PDB/app/smiles-to-pdb
  • SMILES to SDF/app/smiles-to-sdf
  • SMINA/app/smina
  • SMRTnet/app/smrtnet
  • SolubleMPNN/app/soluble-mpnn
  • SPRINT/app/sprint
  • StringZilla v5/app/stringzilla
  • Structural alert screening/app/toxicity-prediction
  • SuperWater/app/superwater
  • SurfDock/app/surfdock

T

  • TAP2/app/tap2
  • TEMPL Pipeline/app/templ-pipeline
  • ThermoMPNN/app/thermompnn
  • Three-to-one converter/app/three-to-one
  • TLimmuno2/app/tlimmuno2
  • TNP/app/tnp
  • TXT to FASTA converter/app/txt-to-fasta

U

  • UniProt Download/app/uniprot-download
  • USAlign/app/usalign

V

  • Veber's rule/app/vebers-rule
  • ViennaRNA/app/viennarna
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