kinfold

name	kinfold
description	Use when simulating stochastic folding kinetics of single-stranded nucleic acids, computing first passage times between structures, or analyzing RNA/DNA folding trajectories.
disable-model-invocation	true
user-invocable	true

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

1. 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 needed
3. 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