protein-docking-configurator

Prepare input files for molecular docking software, automatically determine Grid Box center and size. Supports AutoDock Vina, AutoDock4, and other mainstream docking tools.

Install with Tessl CLI

npx tessl i github:aipoch/medical-research-skills --skill protein-docking-configurator

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Review — 66%

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Learn more

Validation — 10 / 11 Passed

Validation for skill structure

SKILL.md

Review

Evals

Evaluation results

100%

Virtual Screening Grid Box Setup for Kinase Target

Vina config from active site residues

Criteria

Without context

With context

Script invocation

100%

Active site flag

100%

Residue chain format

100%

Software flag vina

100%

Exhaustiveness value

100%

Center coordinates present

100%

Size fields present

100%

Minimum box size

100%

Receptor entry

100%

Ligand entry

100%

Without context: $0.4359 · 1m 44s · 13 turns · 17 in / 7,928 out tokens

With context: $0.5355 · 1m 49s · 24 turns · 62 in / 5,169 out tokens

97%

-3%

AutoDock4 Grid Preparation for Bromodomain Docking Campaign

AutoDock4 GPF from reference ligand

Criteria

Without context

With context

Script invocation

100%

62%

Reference ligand flag

100%

Software autodock4

100%

GPF file extension

100%

Spacing value

100%

Even npts values

100%

Minimum npts

100%

Receptor atom types

100%

Ligand atom types with Cl

100%

Gridcenter field

100%

Without context: $0.5068 · 1m 49s · 17 turns · 24 in / 7,851 out tokens

With context: $0.7241 · 1m 57s · 33 turns · 187 in / 6,467 out tokens

100%

Automated Docking Configuration Pipeline

Python module DockingConfigurator API

Criteria

Without context

With context

Correct import path

100%

No subprocess usage

100%

DockingConfigurator instantiation

100%

Site or ligand method

100%

write_vina_config call

100%

write_autodock4_gpf call

100%

Exhaustiveness 32

100%

Spacing 0.375

100%

Vina config output

100%

AutoDock4 GPF output

100%

Without context: $0.6924 · 2m 17s · 26 turns · 30 in / 10,154 out tokens

With context: $0.5977 · 1m 47s · 26 turns · 212 in / 6,001 out tokens

Evaluated: about 11 hours ago
Agent: Claude Code

Table of Contents

Virtual Screening Grid Box Setup for Kinase Target AutoDock4 Grid Preparation for Bromodomain Docking Campaign Automated Docking Configuration Pipeline

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