Results for “protein-simulation”

18 skills

molecular-dynamics

Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (RMSD, RMSF, contact maps, free energy surfaces).

30.2k · bundle

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botany-based-simulation

Botany Based Simulation Skill

alphagbm-pnl-simulator

Simulates profit and loss for option positions across underlying price, implied volatility, and time to expiration, generating diagrams, breakeven analysis, and probability distributions.

Predict 3D binding poses of small molecule ligands to protein targets using diffusion-based molecular docking, supporting single complexes, batch processing, and virtual screening.

30.2k · bundle

Use when searching protein sequences against profile hidden Markov models (HMMs) such as Pfam or other HMM databases.

Use when searching one or more protein query sequences against a protein sequence database with HMMER's one-pass sequence-vs-sequence searcher.

Use when simulating stochastic folding kinetics of single-stranded nucleic acids, computing first passage times between structures, or analyzing RNA/DNA folding trajectories.

algebra-based-simulation

Algebra Based Simulation Skill

Use when searching protein query sequences against a translated nucleotide database to identify protein-coding regions or homologs in genomic data.

Use when comparing protein sequences against protein databases for similarity searches, homology detection, or functional annotation.

glycoengineering

Analyze and engineer protein glycosylation by scanning sequences for N-glycosylation sequons, predicting O-glycosylation hotspots, and accessing curated glycoengineering tools for therapeutic antibody optimization and vaccine design.

30.2k · bundle

Creates 3Blue1Brown-style animated explainer videos, algorithm visualizations, and math animations using Manim Community Edition.

Manim CE animations: 3Blue1Brown math/algo videos.

paper-review-sim

Simulates a NeurIPS/SC/ICSE-style peer review with five reviewer personas (HPC, ML, Stats, Reproducibility, Devil's Advocate) that verify every claim against actual result data before submission.

openclip-an-open-source-implementation-of-clip-arxiv-2212-07

OpenCLIP: An Open Source Implementation of CLIP

Manim CE animations: 3Blue1Brown math/algo videos.

large-cell-ratio-matching

MaxFuse parameter tuning for datasets with large protein:RNA cell ratios (>100:1)

Use when comparing translated nucleotide query sequences against protein databases to identify homologous proteins and potential protein-coding regions.