Commit 39a6e97
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|---|---|---|---|
@@ -24,7 +24,7 @@ Book 4: [The Genomics Module](genomics/README.md), working with genomic data. | |||
| 24 | 24 | ||
| 25 | 25 | Book 5: [The Protein-Disorder Module](protein-disorder/README.md), predicting protein-disorder. | |
| 26 | 26 | ||
| 27 | - Book 6: [The ModFinder Module](modfinder/README.md), identifying potein modifications in 3D structures | ||
| 27 | + Book 6: [The ModFinder Module](modfinder/README.md), identifying protein modifications in 3D structures | ||
| 28 | 28 | ||
| 29 | 29 | ## License | |
| 30 | 30 | ||
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@@ -153,7 +153,7 @@ List<Structure> bioAssemblies = StructureIO.getBiologicalAssemblies(pdbId); | |||
| 153 | 153 | ||
| 154 | 154 | ## Further Reading | |
| 155 | 155 | ||
| 156 | - The RCSB PDB web site has a great [tutorial on Biological Assemblies](http://www.rcsb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html). | ||
| 156 | + The RCSB PDB web site has a great [tutorial on Biological Assemblies](https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies). | ||
| 157 | 157 | ||
| 158 | 158 | <!--automatically generated footer--> | |
| 159 | 159 | ||
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@@ -10,8 +10,8 @@ Secondary structure can be formally defined by the pattern of hydrogen bonds of | |||
| 10 | 10 | More specifically, the secondary structure is defined by the patterns of hydrogen bonds formed between | |
| 11 | 11 | amine hydrogen (-NH) and carbonyl oxygen (C=O) atoms contained in the backbone peptide bonds of the protein. | |
| 12 | 12 | ||
| 13 | - For more info see the Wikipedia article on [protein secondary structure] | ||
| 14 | - (https://en.wikipedia.org/wiki/Protein_secondary_structure). | ||
| 13 | + For more info see the Wikipedia article | ||
| 14 | + on [protein secondary structure](https://en.wikipedia.org/wiki/Protein_secondary_structure). | ||
| 15 | 15 | ||
| 16 | 16 | ## Secondary Structure Annotation | |
| 17 | 17 | ||
@@ -106,8 +106,8 @@ input Structure overriding any previous annotation, like in the DSSPParser. An e | |||
| 106 | 106 | ssp.calculate(s, true); //true assigns the SS to the Structure | |
| 107 | 107 | ``` | |
| 108 | 108 | ||
| 109 | - BioJava Class: [org.biojava.nbio.structure.secstruc.SecStrucCalc] | ||
| 110 | - (http://www.biojava.org/docs/api/org/biojava/nbio/structure/secstruc/SecStrucCalc.html) | ||
| 109 | + BioJava Class: | ||
| 110 | + [org.biojava.nbio.structure.secstruc.SecStrucCalc](http://www.biojava.org/docs/api/org/biojava/nbio/structure/secstruc/SecStrucCalc.html) | ||
| 111 | 111 | ||
| 112 | 112 | ### Storage and Data Structures | |
| 113 | 113 | ||
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