How do I install the Kinfold skill?

Run npx skillmds@latest add vimalinx/kinfold in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Kinfold safe to use?

This skill has not completed SkillMD's automated safety review yet. Independent scanners report: SkillSpector: PASS, Skill Scanner: PASS. Capability flags: docs only. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Kinfold?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Kinfold free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Kinfold?

vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Kinfold by vimalinx — Agent Skill

Name: Kinfold
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

kinfold

Quick Start

Command: Kinfold [OPTION]... < input.fa
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/Kinfold
Full reference: See references/help.md for complete options and details

When To Use This Tool

Simulate stochastic RNA/DNA folding trajectories instead of only equilibrium structures.
Estimate first-passage or recurrence times between structures.
Explore co-transcriptional growth effects with chain-extension parameters.
Output only local minima or low-energy states from kinetic runs.

Common Patterns

# 1) Run multiple stochastic trajectories from an open chain
printf 'GGGAAAUCC\n' | Kinfold --num=100 --time=1000

# 2) Use explicit start and stop structures for first-passage simulations
printf 'GGGAAAUCC\n.........\n(((...)))\n' | Kinfold --start --stop --fpt

# 3) Simulate co-transcriptional growth and print local minima only
printf 'GGGAAAUCC\n' | Kinfold --grow=5 --glen=10 --lmin

Recommended Workflow

Prepare input file with sequence (required), start structure (if using --start), and stop structures (if using --stop)
Set simulation parameters: temperature (-T), max time (--time), number of trajectories (--num), and random seed (--seed) as needed
Configure energy model options: dangling ends (-d), multiloop energies (--logML), and move set constraints (--noShift, --noLP)
Run simulation and interpret output: first passage times (default), local minima (--lmin), or structures within energy cutoff (--cut)

Guardrails

Input file must start with sequence line; start/stop structures require --start/--stop flags respectively
Default simulation runs 1 trajectory for 500 time units; increase --num and --time for adequate sampling
Use --noLP to avoid biologically unrealistic structures with isolated base pairs

---name: kinfolddescription: Use when simulating stochastic folding kinetics of single-stranded nucleic acids, computing first passage times between structures, or analyzing RNA/DNA folding trajectories.---# kinfold## Quick Start- **Command**: `Kinfold [OPTION]... < input.fa`- **Local executable**: `/home/vimalinx/miniforge3/envs/bio/bin/Kinfold`- **Full reference**: See `references/help.md` for complete options and details## When To Use This Tool- Simulate stochastic RNA/DNA folding trajectories instead of only equilibrium structures.- Estimate first-passage or recurrence times between structures.- Explore co-transcriptional growth effects with chain-extension parameters.- Output only local minima or low-energy states from kinetic runs.## Common Patterns```bash# 1) Run multiple stochastic trajectories from an open chainprintf 'GGGAAAUCC\n' | Kinfold --num=100 --time=1000``````bash# 2) Use explicit start and stop structures for first-passage simulationsprintf 'GGGAAAUCC\n.........\n(((...)))\n' | Kinfold --start --stop --fpt``````bash# 3) Simulate co-transcriptional growth and print local minima onlyprintf 'GGGAAAUCC\n' | Kinfold --grow=5 --glen=10 --lmin```## Recommended Workflow1. Prepare input file with sequence (required), start structure (if using `--start`), and stop structures (if using `--stop`)2. Set simulation parameters: temperature (`-T`), max time (`--time`), number of trajectories (`--num`), and random seed (`--seed`) as needed3. Configure energy model options: dangling ends (`-d`), multiloop energies (`--logML`), and move set constraints (`--noShift`, `--noLP`)4. Run simulation and interpret output: first passage times (default), local minima (`--lmin`), or structures within energy cutoff (`--cut`)## Guardrails- Input file must start with sequence line; start/stop structures require `--start`/`--stop` flags respectively- Default simulation runs 1 trajectory for 500 time units; increase `--num` and `--time` for adequate sampling- Use `--noLP` to avoid biologically unrealistic structures with isolated base pairs

Frequently asked questions

Kinfold