# REDUCE

> a program for adding hydrogens to a Protein DataBank (PDB) molecular structure file

**Wikidata**: [Q114840896](https://www.wikidata.org/wiki/Q114840896)  
**Source**: https://4ort.xyz/entity/reduce-q114840896

## Summary
REDUCE is a software program used to add hydrogen atoms to Protein DataBank (PDB) molecular structure files. It is widely utilized in structural biology and computational chemistry for preparing protein structures for further analysis. The program was developed by Anthony C. Hearn and first described in a 1989 paper.

## Key Facts
- Instance of: Software
- Primary function: Adds hydrogen atoms to PDB-format molecular structure files
- Creator: Anthony C. Hearn, Australian-American computer scientist and physicist
- First described in publication: “Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation” (1989)
- Used in structural biology and computational modeling workflows
- Operates within the domain of macromolecular structure processing
- Sitelink count: High cross-linking across scientific databases indicates widespread use and recognition

## FAQs
### Q: What is REDUCE used for?
A: REDUCE is used to add hydrogen atoms to PDB-format molecular structure files. This process is essential for preparing accurate models of proteins for computational simulations, visualization, and structural analysis.

### Q: Who created REDUCE?
A: REDUCE was created by Anthony C. Hearn, an Australian-American physicist and computer scientist known for his work in symbolic computation and molecular modeling.

### Q: Where can I find documentation or the original paper for REDUCE?
A: REDUCE was first introduced in the 1989 publication titled *“Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation.”* Documentation may also be found through bioinformatics resources or software repositories associated with structural biology tools.

## Why It Matters
REDUCE plays a critical role in structural biology by enabling researchers to generate complete atomic models from incomplete experimental data. Many crystallographic methods do not resolve hydrogen atom positions due to their low electron density, but these atoms are crucial for accurate molecular modeling, hydrogen bonding predictions, and force-field-based simulations. By automating the addition of hydrogens based on chemical rules and geometric considerations, REDUCE improves the fidelity of biomolecular structures used in drug design, enzyme mechanism studies, and molecular dynamics simulations. Its integration into standard structural biology pipelines has made it an indispensable tool in both academic and industrial research environments.

## Notable For
- One of the earliest programs designed specifically for hydrogen addition to PDB files
- Based on rigorous physical and chemical principles outlined in peer-reviewed literature
- Developed by Anthony C. Hearn, a notable figure in computer algebra systems and symbolic computation
- Widely adopted in structural biology and integrated into major molecular visualization and simulation platforms
- Frequent citation and usage in high-impact structural biology and computational chemistry research

## Body

### Overview
REDUCE is a specialized software application intended for use in structural biology. Its core functionality involves predicting and inserting hydrogen atoms into macromolecular structures stored in the Protein DataBank (PDB) format. These structures often lack explicit hydrogen coordinates due to limitations in X-ray crystallography and other structure determination techniques.

### Development and History
- Created by Anthony C. Hearn, who held dual citizenship in Australia and the United States
- Professionally active as a physicist, computer scientist, and university teacher
- First formally presented in a 1989 article that detailed the methodological basis for assigning hydrogen positions, particularly for asparagine and glutamine residues
- Built upon earlier work in symbolic computation and molecular mechanics

### Technical Functionality
- Processes PDB-formatted input files
- Applies chemical and stereochemical rules to determine optimal placement of hydrogen atoms
- Particularly effective at resolving ambiguous orientations of polar side chains such as Asn and Gln
- Outputs updated PDB files with added hydrogen coordinates suitable for downstream applications like molecular dynamics or docking studies

### Integration and Usage
- Commonly incorporated into pre-processing pipelines for molecular modeling tasks
- Supported by various structural biology software suites and visualization tools
- Frequently cited in publications involving refined protein structures and computational modeling
- Maintained relevance over decades due to accuracy and utility in handling missing hydrogen information in biomolecular datasets