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1 | | -The Protein Structure Modules of BioJava |
| 1 | +The Structure Modules of BioJava |
2 | 2 | ===================================================== |
3 | 3 |
|
4 | | -A tutorial for the protein structure modules of [BioJava](http://www.biojava.org) |
| 4 | +A tutorial for the structure modules of [BioJava](http://www.biojava.org) |
5 | 5 |
|
6 | 6 | ## About |
7 | 7 | <table> |
@@ -32,35 +32,35 @@ Chapter 1 - Quick [Installation](installation.md) |
32 | 32 |
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33 | 33 | Chapter 2 - [First Steps](firststeps.md) |
34 | 34 |
|
35 | | -Chapter 3 - The [data model](structure-data-model.md) for the representation of macromolecular structures. |
| 35 | +Chapter 3 - The [Structure Data Model](structure-data-model.md), for the representation of macromolecular structures |
36 | 36 |
|
37 | | -Chapter 4 - [Local installations](caching.md) of PDB |
| 37 | +Chapter 4 - [Local Installations](caching.md) of PDB |
38 | 38 |
|
39 | 39 | Chapter 5 - The [Chemical Component Dictionary](chemcomp.md) |
40 | 40 |
|
41 | | -Chapter 6 - How to [work with mmCIF/PDBx files](mmcif.md) |
| 41 | +Chapter 6 - How to [Work with mmCIF/PDBx Files](mmcif.md) |
42 | 42 |
|
43 | | -Chapter 7 - [SEQRES and ATOM records](seqres.md), mapping to Uniprot (SIFTs) |
| 43 | +Chapter 7 - [SEQRES and ATOM Records](seqres.md), mapping to Uniprot (SIFTs) |
44 | 44 |
|
45 | | -Chapter 8 - Protein [Structure Alignments](alignment.md) |
| 45 | +Chapter 8 - [Structure Alignments](alignment.md) |
46 | 46 |
|
47 | 47 | Chapter 9 - [Biological Assemblies](bioassembly.md) |
48 | 48 |
|
49 | 49 | Chapter 10 - [External Databases](externaldb.md) like SCOP & CATH |
50 | 50 |
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51 | 51 | Chapter 11 - [Accessible Surface Areas](asa.md) |
52 | 52 |
|
53 | | -Chapter 12 - [Contacts within a chain and between chains](contact-map.md) |
| 53 | +Chapter 12 - [Contacts Within a Chain and between Chains](contact-map.md) |
54 | 54 |
|
55 | | -Chapter 13 - Finding all interfaces in crystal: [crystal contacts](crystal-contacts.md) |
| 55 | +Chapter 13 - Finding all Interfaces in Crystal: [Crystal Contacts](crystal-contacts.md) |
56 | 56 |
|
57 | 57 | Chapter 14 - Protein Symmetry |
58 | 58 |
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59 | 59 | Chapter 15 - Bonds |
60 | 60 |
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61 | 61 | Chapter 16 - [Special Cases](special.md) |
62 | 62 |
|
63 | | -Chapter 17 - [Lists](lists.md) of PDB IDs and PDB [status information](lists.md). |
| 63 | +Chapter 17 - [Lists](lists.md) of PDB IDs and PDB [Status Information](lists.md) |
64 | 64 |
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65 | 65 |
|
66 | 66 | ### Author: |
@@ -88,7 +88,7 @@ The content of this tutorial is available under the [CC-BY](http://creativecommo |
88 | 88 |
|
89 | 89 | Navigation: |
90 | 90 | [Home](../README.md) |
91 | | -| Book 3: The Protein Structure modules |
| 91 | +| Book 3: The Structure modules |
92 | 92 |
|
93 | 93 | Prev: [Book 2: The Alignment module](../alignment/README.md) |
94 | 94 |
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