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Designs PROTACs, molecular glues, and bivalent degraders with explicit handling of E3 ligase choice (VHL, CRBN, IAP, MDM2, KEAP1), linker design (length, composition, rigidity),...

Performs retrosynthetic planning using AiZynthFinder (MCTS, template-based), Chemformer (template-free transformer), ASKCOS, and emerging RetroSynFormer with explicit handling of...

Analyzes chemical libraries by scaffold using Bemis-Murcko scaffolds, generic frameworks, cyclic skeletons, matched molecular pair (MMP) analysis via mmpdb, R-group decomposition,...

Performs 3D shape-based similarity searching using ROCS (OpenEye), USRCAT (ultra-fast), Open3DAlign (RDKit), ESPSim (electrostatic), and ShaEP with explicit handling of...

Performs molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count fingerprints with explicit choice rules for symmetric vs asymmetric...

Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector binding, atom...

Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice rules across rigid vs flexible...

Process many FASTA/FASTQ/GenBank files in batch — merge, split, convert, summarize, organize — using Biopython 1.83+.

Align Illumina short reads to a reference genome with BWA-MEM — including index, MEM algorithm, paired-end, alt-contig handling, and 2026 best practices.

Use BWA-MEM2 — the SIMD-accelerated BWA-MEM replacement — for 2-3x speedup on human genome alignment with identical results to BWA-MEM.

Compute codon usage frequencies, RSCU, CAI, and tRNA adaptation — for gene expression prediction, heterologous expression design, and comparative genomics.

Read and write gzip, bzip2, and BGZF-compressed FASTA/FASTQ using Python stdlib and Biopython — including indexable BGZF.

Access, filter, and trim Phred quality scores in FASTQ reads using Biopython 1.83+ — including per-position profiles and encoding auto-detection.

Filter FASTA/FASTQ records by length, identity, regex on headers, GC window, complexity, and custom predicates — streaming with Biopython 1.83+.

Splice-aware RNA-seq alignment with HISAT2 — fast, memory-efficient, and the default in many bulk RNA-seq pipelines alongside STAR.

Find patterns, motifs, and binding sites in DNA/RNA/protein sequences — using regex, IUPAC patterns, position weight matrices, and modern motif databases (JASPAR 2024, CIS-BP).

Keep R1/R2 reads in lockstep — synchronize iteration, filter pairs together, interleave, and deinterleave — using Biopython and the 2026 best practices.

Programmatically read, modify, filter, and write BAM/CRAM/VCF files using pysam 0.22+ — the Python interface to htslib for NGS I/O, variant calling, and custom pipelines.

Read and write FASTA, FASTQ, GenBank, EMBL using Biopython SeqIO — including indexed random access, conversion, and 2026 best practices.

Compute reverse complements, complements, and strand-aware operations on DNA/RNA — including IUPAC ambiguity support, batch processing, and the orientation trap.