ProteinIQ

SQUARNA is a tool for RNA secondary structure prediction. It can take a single RNA sequence or an alignment of sequences as input. SQUARNA handles pseudoknots and can predict alternative structures. SQUARNA allows structural restraints and chemical probing data as additional input and is available at https://github.com/febos/SQUARNA and https://larnal.imol.institute/.

Use BridgeDb functions and load identifier mapping databases in R. It uses GitHub, Zenodo, and Figshare if you use this package to download identifier mappings files.

This package can generate a synthetic map with reads covering the nucleosome regions as well as a synthetic map with forward and reverse reads emulating next-generation sequencing. The synthetic hybridization data of “Tiling Arrays” can also be generated. The user has choice between three different distributions for the read positioning: Normal, Student and Uniform. In addition, a visualization tool is provided to explore the synthetic nucleosome maps.

A structural pharmacology workbench for cognition-related CNS targets, built so that a displayed number must trace to a computation. Runs Boltz-2 locally for structure prediction, validates chemistry with RDKit, enforces a provenance record on every value, and reports eight studies pre-registered under content hashes before any data was seen. Its headline result is negative: designed peptides did not separate from composition-matched shuffles of their own amino acids.

Local Python sequence utilities for nucleotide composition, DNA and RNA reverse complements, NCBI genetic-code translation, six-frame candidate ORF enumeration, and IUPAC motif searches. Computase accepts raw nucleotide strings or one FASTA record and returns structured, bounded results with explicit scientific conventions.

WarPP predicts the position and orientation of water molecules in small-molecule binding sites. It places and scores water molecules in binding sites of crystallographic structures based on EDIAscorer results and interaction geometries as known from experimentally solved protein structures. WarPP was validated on a high-quality set of 1,500 protein-ligand complexes, containing 20,000 crystallographically observed water molecules. It is sufficiently fast for high-throughput analyses. It correctly places water molecules in approx. 80% of the cases. Users can export the predictions as PDB files for, e.g., molecular docking with JAMDA.