feat: release 3.1.0, replace BioJava, make BPSEQ more robust (#33)

* Reset version to 3.1-SNAPSHOT

* build: bump nexus-staging-maven-plugin from 1.6.7 to 1.6.13

Bumps nexus-staging-maven-plugin from 1.6.7 to 1.6.13.

---
updated-dependencies:
- dependency-name: org.sonatype.plugins:nexus-staging-maven-plugin
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* build: bump slf4j-api from 1.7.36 to 2.0.0

Bumps [slf4j-api](https://github.com/qos-ch/slf4j) from 1.7.36 to 2.0.0.
- [Release notes](https://github.com/qos-ch/slf4j/releases)
- [Commits](qos-ch/slf4j@v_1.7.36...v_2.0.0)

---
updated-dependencies:
- dependency-name: org.slf4j:slf4j-api
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

* build: bump sortpom-maven-plugin from 2.12.0 to 3.2.0

Bumps [sortpom-maven-plugin](https://github.com/Ekryd/sortpom) from 2.12.0 to 3.2.0.
- [Release notes](https://github.com/Ekryd/sortpom/releases)
- [Commits](Ekryd/sortpom@sortpom-parent-2.12.0...sortpom-parent-3.2.0)

---
updated-dependencies:
- dependency-name: com.github.ekryd.sortpom:sortpom-maven-plugin
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

* build: bump jackson-databind from 2.13.2 to 2.13.3

Bumps [jackson-databind](https://github.com/FasterXML/jackson) from 2.13.2 to 2.13.3.
- [Release notes](https://github.com/FasterXML/jackson/releases)
- [Commits](https://github.com/FasterXML/jackson/commits)

---
updated-dependencies:
- dependency-name: com.fasterxml.jackson.core:jackson-databind
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* build: bump maven-gpg-plugin from 1.5 to 3.0.1 (#15)

* build: bump maven-source-plugin from 3.2.0 to 3.2.1 (#14)

* build: bump jackson-annotations from 2.13.2 to 2.13.3 (#16)

* build: bump value from 2.9.0 to 2.9.1 (#13)

* build: bump versions-maven-plugin from 2.8.1 to 2.11.0 (#12)

* feat: replace BioJava dependency (#17)

* Move default implementation one level up in hierarchy

* Set version to 3.0.9

* Reset version to 3.1-SNAPSHOT

* feat: switch to official mmCIF parser in place of BioJava

* build: update version of ciftools-java

* fix: remove spotless, which breaks CI

* fix: set required Java version to 11

* build: bump maven-compiler-plugin from 3.8.1 to 3.10.1 (#24)

Bumps [maven-compiler-plugin](https://github.com/apache/maven-compiler-plugin) from 3.8.1 to 3.10.1.
- [Release notes](https://github.com/apache/maven-compiler-plugin/releases)
- [Commits](apache/maven-compiler-plugin@maven-compiler-plugin-3.8.1...maven-compiler-plugin-3.10.1)

---
updated-dependencies:
- dependency-name: org.apache.maven.plugins:maven-compiler-plugin
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* build: bump maven-dependency-plugin from 3.1.2 to 3.3.0 (#25)

Bumps [maven-dependency-plugin](https://github.com/apache/maven-dependency-plugin) from 3.1.2 to 3.3.0.
- [Release notes](https://github.com/apache/maven-dependency-plugin/releases)
- [Commits](apache/maven-dependency-plugin@maven-dependency-plugin-3.1.2...maven-dependency-plugin-3.3.0)

---
updated-dependencies:
- dependency-name: org.apache.maven.plugins:maven-dependency-plugin
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* build: bump maven-javadoc-plugin from 3.2.0 to 3.4.1 (#23)

Bumps [maven-javadoc-plugin](https://github.com/apache/maven-javadoc-plugin) from 3.2.0 to 3.4.1.
- [Release notes](https://github.com/apache/maven-javadoc-plugin/releases)
- [Commits](apache/maven-javadoc-plugin@maven-javadoc-plugin-3.2.0...maven-javadoc-plugin-3.4.1)

---
updated-dependencies:
- dependency-name: org.apache.maven.plugins:maven-javadoc-plugin
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* build: bump actions/checkout from 2 to 3 (#22)

Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 3.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v2...v3)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* build: bump actions/setup-java from 1 to 3 (#20)

* build: bump actions/setup-java from 1 to 3

Bumps [actions/setup-java](https://github.com/actions/setup-java) from 1 to 3.
- [Release notes](https://github.com/actions/setup-java/releases)
- [Commits](actions/setup-java@v1...v3)

---
updated-dependencies:
- dependency-name: actions/setup-java
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

* build: bump actions/setup-java from 1 to 3

Bumps [actions/setup-java](https://github.com/actions/setup-java) from 1 to 3.
- [Release notes](https://github.com/actions/setup-java/releases)
- [Commits](actions/setup-java@v1...v3)

---
updated-dependencies:
- dependency-name: actions/setup-java
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

* fix: add distribution info to GitHub Actions config

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Tomasz Zok <[email protected]>

* build: bump logback-classic from 1.2.11 to 1.4.0 (#21)

Bumps [logback-classic](https://github.com/qos-ch/logback) from 1.2.11 to 1.4.0.
- [Release notes](https://github.com/qos-ch/logback/releases)
- [Commits](qos-ch/logback@v_1.2.11...v_1.4.0)

---
updated-dependencies:
- dependency-name: ch.qos.logback:logback-classic
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* build: bump jackson-annotations from 2.13.3 to 2.13.4 (#28)

* build: bump jackson-databind from 2.13.3 to 2.13.4 (#27)

* build: bump value from 2.9.1 to 2.9.2 (#30)

* build: bump versions-maven-plugin from 2.11.0 to 2.12.0 (#29)

* feat: add spotless plugin (#31)

* feat: add spotless configuration

* ref: auto-refactor using spotless

* feat: make bpseq class more robust (#32)

* feat: add a failing test case

* feat: enable debug logging during tests

* feat: detect invalid situation in which a base pair is made of an unknown residue

* ref: improve error message

* feat: fix the test case to expect the exception

* Reset version to 3.1-SNAPSHOT

* build: bump nexus-staging-maven-plugin from 1.6.7 to 1.6.13

Bumps nexus-staging-maven-plugin from 1.6.7 to 1.6.13.

---
updated-dependencies:
- dependency-name: org.sonatype.plugins:nexus-staging-maven-plugin
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* build: bump slf4j-api from 1.7.36 to 2.0.0

Bumps [slf4j-api](https://github.com/qos-ch/slf4j) from 1.7.36 to 2.0.0.
- [Release notes](https://github.com/qos-ch/slf4j/releases)
- [Commits](qos-ch/slf4j@v_1.7.36...v_2.0.0)

---
updated-dependencies:
- dependency-name: org.slf4j:slf4j-api
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

* build: bump sortpom-maven-plugin from 2.12.0 to 3.2.0

Bumps [sortpom-maven-plugin](https://github.com/Ekryd/sortpom) from 2.12.0 to 3.2.0.
- [Release notes](https://github.com/Ekryd/sortpom/releases)
- [Commits](Ekryd/sortpom@sortpom-parent-2.12.0...sortpom-parent-3.2.0)

---
updated-dependencies:
- dependency-name: com.github.ekryd.sortpom:sortpom-maven-plugin
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

* build: bump maven-gpg-plugin from 1.5 to 3.0.1 (#15)

* build: bump maven-source-plugin from 3.2.0 to 3.2.1 (#14)

* build: bump jackson-annotations from 2.13.2 to 2.13.3 (#16)

* build: bump value from 2.9.0 to 2.9.1 (#13)

* build: bump versions-maven-plugin from 2.8.1 to 2.11.0 (#12)

* feat: replace BioJava dependency (#17)

* Move default implementation one level up in hierarchy

* Set version to 3.0.9

* Reset version to 3.1-SNAPSHOT

* feat: switch to official mmCIF parser in place of BioJava

* build: update version of ciftools-java

* fix: remove spotless, which breaks CI

* fix: set required Java version to 11

* build: bump maven-compiler-plugin from 3.8.1 to 3.10.1 (#24)

Bumps [maven-compiler-plugin](https://github.com/apache/maven-compiler-plugin) from 3.8.1 to 3.10.1.
- [Release notes](https://github.com/apache/maven-compiler-plugin/releases)
- [Commits](apache/maven-compiler-plugin@maven-compiler-plugin-3.8.1...maven-compiler-plugin-3.10.1)

---
updated-dependencies:
- dependency-name: org.apache.maven.plugins:maven-compiler-plugin
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* build: bump maven-dependency-plugin from 3.1.2 to 3.3.0 (#25)

Bumps [maven-dependency-plugin](https://github.com/apache/maven-dependency-plugin) from 3.1.2 to 3.3.0.
- [Release notes](https://github.com/apache/maven-dependency-plugin/releases)
- [Commits](apache/maven-dependency-plugin@maven-dependency-plugin-3.1.2...maven-dependency-plugin-3.3.0)

---
updated-dependencies:
- dependency-name: org.apache.maven.plugins:maven-dependency-plugin
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* build: bump maven-javadoc-plugin from 3.2.0 to 3.4.1 (#23)

Bumps [maven-javadoc-plugin](https://github.com/apache/maven-javadoc-plugin) from 3.2.0 to 3.4.1.
- [Release notes](https://github.com/apache/maven-javadoc-plugin/releases)
- [Commits](apache/maven-javadoc-plugin@maven-javadoc-plugin-3.2.0...maven-javadoc-plugin-3.4.1)

---
updated-dependencies:
- dependency-name: org.apache.maven.plugins:maven-javadoc-plugin
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* build: bump actions/checkout from 2 to 3 (#22)

Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 3.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v2...v3)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* build: bump actions/setup-java from 1 to 3 (#20)

* build: bump actions/setup-java from 1 to 3

Bumps [actions/setup-java](https://github.com/actions/setup-java) from 1 to 3.
- [Release notes](https://github.com/actions/setup-java/releases)
- [Commits](actions/setup-java@v1...v3)

---
updated-dependencies:
- dependency-name: actions/setup-java
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

* build: bump actions/setup-java from 1 to 3

Bumps [actions/setup-java](https://github.com/actions/setup-java) from 1 to 3.
- [Release notes](https://github.com/actions/setup-java/releases)
- [Commits](actions/setup-java@v1...v3)

---
updated-dependencies:
- dependency-name: actions/setup-java
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

* fix: add distribution info to GitHub Actions config

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Tomasz Zok <[email protected]>

* build: bump logback-classic from 1.2.11 to 1.4.0 (#21)

Bumps [logback-classic](https://github.com/qos-ch/logback) from 1.2.11 to 1.4.0.
- [Release notes](https://github.com/qos-ch/logback/releases)
- [Commits](qos-ch/logback@v_1.2.11...v_1.4.0)

---
updated-dependencies:
- dependency-name: ch.qos.logback:logback-classic
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* build: bump jackson-annotations from 2.13.3 to 2.13.4 (#28)

* build: bump jackson-databind from 2.13.3 to 2.13.4 (#27)

* build: bump value from 2.9.1 to 2.9.2 (#30)

* build: bump versions-maven-plugin from 2.11.0 to 2.12.0 (#29)

* feat: add spotless plugin (#31)

* feat: add spotless configuration

* ref: auto-refactor using spotless

* feat: make bpseq class more robust (#32)

* feat: add a failing test case

* feat: enable debug logging during tests

* feat: detect invalid situation in which a base pair is made of an unknown residue

* ref: improve error message

* feat: fix the test case to expect the exception

* chore: update version to 3.1.0

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

.github/workflows/maven.yml

@@ -15,10 +15,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up JDK 1.8
-      uses: actions/setup-java@v1
+    - uses: actions/checkout@v3
+    - name: Set up JDK 11
+      uses: actions/setup-java@v3
       with:
-        java-version: 1.8
+        java-version: 11
+        distribution: temurin
     - name: Build with Maven
       run: mvn -B package --file pom.xml

README.md

@@ -13,7 +13,7 @@ You can use BioCommons by adding the following to your `pom.xml`:
 <dependency>
   <groupId>pl.poznan.put</groupId>
   <artifactId>BioCommons</artifactId>
-  <version>3.0.9</version>
+  <version>3.1.0</version>
 </dependency>
 ```
 
@@ -69,8 +69,8 @@ You can find examples and HOWTOs in the
 RNA-Puzzles Toolkit: A Computational Resource of RNA 3d Structure
 Benchmark Datasets, Structure Manipulation and Evaluation Tools. M.
 Magnus, M. Antczak, T. Zok, J. Wiedemann, P. Lukasiak, Y. Cao, J.M.
-Bujnicki, E. Westhof, M. Szachniuk and Z. Miao. *Nucleic Acids
-Research*. 2020. 48(2):576–588.
+Bujnicki, E. Westhof, M. Szachniuk, Z. Miao. *Nucleic Acids Research*.
+2020. 48(2):576–588.
 doi:[10.1093/nar/gkz1108](https://doi.org/10.1093/nar/gkz1108)
 
 </div>
@@ -79,7 +79,7 @@ doi:[10.1093/nar/gkz1108](https://doi.org/10.1093/nar/gkz1108)
 
 RNAvista: A Webserver to Assess RNA Secondary Structures with
 Non-Canonical Base Pairs. M. Antczak, M. Zablocki, T. Zok, A. Rybarczyk,
-J. Blazewicz and M. Szachniuk. *Bioinformatics*. 2019. 35(1):152–155.
+J. Blazewicz, M. Szachniuk. *Bioinformatics*. 2019. 35(1):152–155.
 doi:[10.1093/bioinformatics/bty609](https://doi.org/10.1093/bioinformatics/bty609)
 
 </div>
@@ -88,16 +88,16 @@ doi:[10.1093/bioinformatics/bty609](https://doi.org/10.1093/bioinformatics/bty60
 
 RNAfitme: A Webserver for Modeling Nucleobase and Nucleoside Residue
 Conformation in Fixed-Backbone RNA Structures. M. Antczak, T. Zok, M.
-Osowiecki, M. Popenda, R.W. Adamiak and M. Szachniuk. *BMC
-Bioinformatics*. 2018. 19(1):304.
+Osowiecki, M. Popenda, R.W. Adamiak, M. Szachniuk. *BMC Bioinformatics*.
+2018. 19(1):304.
 doi:[10.1186/s12859-018-2317-9](https://doi.org/10.1186/s12859-018-2317-9)
 
 </div>
 
 <div id="ref-Zok2018" class="csl-entry">
 
 RNApdbee 2.0: Multifunctional Tool for RNA Structure Annotation. T. Zok,
-M. Antczak, M. Zurkowski, M. Popenda, J. Blazewicz, R.W. Adamiak and M.
+M. Antczak, M. Zurkowski, M. Popenda, J. Blazewicz, R.W. Adamiak, M.
 Szachniuk. *Nucleic Acids Research*. 2018. 46(W1):W30–W35.
 doi:[10.1093/nar/gky314](https://doi.org/10.1093/nar/gky314)
 
@@ -107,15 +107,15 @@ doi:[10.1093/nar/gky314](https://doi.org/10.1093/nar/gky314)
 
 New Algorithms to Represent Complex Pseudoknotted RNA Structures in
 Dot-Bracket Notation. M. Antczak, M. Popenda, T. Zok, M. Zurkowski, R.W.
-Adamiak and M. Szachniuk. *Bioinformatics*. 2018. 34(8):1304–1312.
+Adamiak, M. Szachniuk. *Bioinformatics*. 2018. 34(8):1304–1312.
 doi:[10.1093/bioinformatics/btx783](https://doi.org/10.1093/bioinformatics/btx783)
 
 </div>
 
 <div id="ref-Wiedemann2017" class="csl-entry">
 
 LCS-TA to Identify Similar Fragments in RNA 3d Structures. J. Wiedemann,
-T. Zok, M. Milostan and M. Szachniuk. *BMC Bioinformatics*. 2017.
+T. Zok, M. Milostan, M. Szachniuk. *BMC Bioinformatics*. 2017.
 18(1):456.
 doi:[10.1186/s12859-017-1867-6](https://doi.org/10.1186/s12859-017-1867-6)
 
@@ -125,7 +125,7 @@ doi:[10.1186/s12859-017-1867-6](https://doi.org/10.1186/s12859-017-1867-6)
 
 New in Silico Approach to Assess RNA Secondary Structures with
 Non-Canonical Base Pairs. A. Rybarczyk, N. Szostak, M. Antczak, T. Zok,
-M. Popenda, R.W. Adamiak, J. Blazewicz and M. Szachniuk. *BMC
+M. Popenda, R.W. Adamiak, J. Blazewicz, M. Szachniuk. *BMC
 Bioinformatics*. 2015. 16(1):276.
 doi:[10.1186/s12859-015-0718-6](https://doi.org/10.1186/s12859-015-0718-6)
 
@@ -135,16 +135,16 @@ doi:[10.1186/s12859-015-0718-6](https://doi.org/10.1186/s12859-015-0718-6)
 
 Building the Library of RNA 3d Nucleotide Conformations Using Clustering
 Approach. T. Zok, M. Antczak, M. Riedel, D. Nebel, T. Villmann, P.
-Lukasiak, J. Blazewicz and M. Szachniuk. *International Journal of
-Applied Mathematics and Computer Science*. 2015. 25(3):689–700.
+Lukasiak, J. Blazewicz, M. Szachniuk. *International Journal of Applied
+Mathematics and Computer Science*. 2015. 25(3):689–700.
 doi:[10.1515/amcs-2015-0050](https://doi.org/10.1515/amcs-2015-0050)
 
 </div>
 
 <div id="ref-Zok2014" class="csl-entry">
 
 MCQ4Structures to Compute Similarity of Molecule Structures. T. Zok, M.
-Popenda and M. Szachniuk. *Central European Journal of Operations
+Popenda, M. Szachniuk. *Central European Journal of Operations
 Research*. 2014. 22(3):457–473.
 doi:[10.1007/s10100-013-0296-5](https://doi.org/10.1007/s10100-013-0296-5)
 
@@ -154,24 +154,24 @@ doi:[10.1007/s10100-013-0296-5](https://doi.org/10.1007/s10100-013-0296-5)
 
 RNApdbee – a Webserver to Derive Secondary Structures from Pdb Files of
 Knotted and Unknotted RNAs. M. Antczak, T. Zok, M. Popenda, P. Lukasiak,
-R.W. Adamiak, J. Blazewicz and M. Szachniuk. *Nucleic Acids Research*.
+R.W. Adamiak, J. Blazewicz, M. Szachniuk. *Nucleic Acids Research*.
 2014. 42(W1):W368–W372.
 doi:[10.1093/nar/gku330](https://doi.org/10.1093/nar/gku330)
 
 </div>
 
 <div id="ref-Keating2011" class="csl-entry">
 
-A New Way to See RNA. K.S. Keating, E.L. Humphris and A.M. Pyle.
-*Quarterly Reviews of Biophysics*. 2011. 44(4):433–466.
+A New Way to See RNA. K.S. Keating, E.L. Humphris, A.M. Pyle. *Quarterly
+Reviews of Biophysics*. 2011. 44(4):433–466.
 doi:[10.1017/S0033583511000059](https://doi.org/10.1017/S0033583511000059)
 
 </div>
 
 <div id="ref-Zirbel2009" class="csl-entry">
 
 Classification and Energetics of the Base-Phosphate Interactions in RNA.
-C.L. Zirbel, J.E. Šponer, J. Šponer, J. Stombaugh and N.B. Leontis.
+C.L. Zirbel, J.E. Šponer, J. Šponer, J. Stombaugh, N.B. Leontis.
 *Nucleic Acids Research*. 2009. 37(15):4898–4918.
 doi:[10.1093/nar/gkp468](https://doi.org/10.1093/nar/gkp468)
 
@@ -180,7 +180,7 @@ doi:[10.1093/nar/gkp468](https://doi.org/10.1093/nar/gkp468)
 <div id="ref-Smit2008" class="csl-entry">
 
 From Knotted to Nested RNA Structures: A Variety of Computational
-Methods for Pseudoknot Removal. S. Smit, K. Rother, J. Heringa and R.
+Methods for Pseudoknot Removal. S. Smit, K. Rother, J. Heringa, R.
 Knight. *RNA*. 2008. 14(3):410–416.
 doi:[10.1261/rna.881308](https://doi.org/10.1261/rna.881308)
 
@@ -189,7 +189,7 @@ doi:[10.1261/rna.881308](https://doi.org/10.1261/rna.881308)
 <div id="ref-Leontis2001" class="csl-entry">
 
 Geometric Nomenclature and Classification of RNA Base Pairs. N.B.
-Leontis and E. Westhof. *RNA*. 2001. 7(4):499–512.
+Leontis, E. Westhof. *RNA*. 2001. 7(4):499–512.
 doi:[10.1017/S1355838201002515](https://doi.org/10.1017/S1355838201002515)
 
 </div>