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Cover Image

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Cover Image

  • First Published: 07 January 2022
Cover Image

Still image from the video Opioids and Pain Signaling of a neuronal synapse with vesicles and relevant proteins highlighted. See article by Zardecki et al., pp. 129–140.

Issue Information

Free Access

Issue information

  • Pages: 1-4
  • First Published: 07 January 2022

Introduction

Free Access

Tools 2022: A compilation of tools for protein science

  • Pages: 5-7
  • First Published: 09 December 2021

Review

Free Access

PANTHER: Making genome-scale phylogenetics accessible to all

Paul D. Thomas,  Dustin Ebert,  Anushya Muruganujan,  Tremayne Mushayahama,  Laurent-Philippe Albou,  Huaiyu Mi, 
  • Pages: 8-22
  • First Published: 30 October 2021

Tools for Protein Science

Free Access

DbStRiPs: Database of structural repeats in proteins

Broto Chakrabarty,  Nita Parekh, 
  • Pages: 23-36
  • First Published: 27 February 2021
Open Access

DichroWeb, a website for calculating protein secondary structure from circular dichroism spectroscopic data

Andrew J. Miles,  Sergio G. Ramalli,  B. A. Wallace, 
  • Pages: 37-46
  • First Published: 02 July 2021
Free Access

KEGG mapping tools for uncovering hidden features in biological data

Minoru Kanehisa,  Yoko Sato,  Masayuki Kawashima, 
  • Pages: 47-53
  • First Published: 23 August 2021
Open Access

SynWiki: Functional annotation of the first artificial organism Mycoplasma mycoides JCVI-syn3A

Tiago Pedreira,  Christoph Elfmann,  Neil Singh,  Jörg Stülke, 
  • Pages: 54-62
  • First Published: 13 September 2021
Free Access

nightshift: A Python program for plotting simulated NMR spectra from assigned chemical shifts from the Biological Magnetic Resonance Data Bank

Ian J. Fucci,  R. Andrew Byrd, 
  • Pages: 63-74
  • First Published: 13 September 2021
Free Access

Compendium of causative genes and their encoded proteins for common monogenic disorders

Tucker L. Apgar,  Charles R. Sanders, 
  • Pages: 75-91
  • First Published: 13 September 2021
Free Access

The evolution of the antimicrobial peptide database over 18 years: Milestones and new features

Guangshun Wang,  C. Michael Zietz,  Ashok Mudgapalli,  Shuona Wang,  Zhe Wang, 
  • Pages: 92-106
  • First Published: 16 September 2021
Free Access

Python-based Helix Indexer: A graphical user interface program for finding symmetry of helical assembly through Fourier–Bessel indexing of electron microscopic data

Xuewu Zhang, 
  • Pages: 107-117
  • First Published: 16 September 2021
Free Access

PANNZER—A practical tool for protein function prediction

Petri Törönen,  Liisa Holm, 
  • Pages: 118-128
  • First Published: 25 September 2021
Free Access

PDB-101: Educational resources supporting molecular explorations through biology and medicine

Christine Zardecki,  Shuchismita Dutta,  David S. Goodsell,  Robert Lowe,  Maria Voigt,  Stephen K. Burley, 
  • Pages: 129-140
  • First Published: 03 October 2021
Open Access

Observed Antibody Space: A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences

Tobias H. Olsen,  Fergus Boyles,  Charlotte M. Deane, 
  • Pages: 141-146
  • First Published: 15 October 2021
Open Access

Match_Motif: A rapid computational tool to assist in protein–protein interaction design

Martin Zacharias, 
  • Pages: 147-157
  • First Published: 14 October 2021
Free Access

SMOG 2 and OpenSMOG: Extending the limits of structure-based models

Antonio B. de Oliveira Jr,  Vinícius G. Contessoto,  Asem Hassan,  Sandra Byju,  Ailun Wang,  Yang Wang,  Esteban Dodero-Rojas,  Udayan Mohanty,  Jeffrey K. Noel,  Jose N. Onuchic,  Paul C. Whitford, 
  • Pages: 158-172
  • First Published: 16 October 2021
Open Access

Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data

Gert-Jan Bekker,  Masashi Yokochi,  Hirofumi Suzuki,  Yasuyo Ikegawa,  Takeshi Iwata,  Takahiro Kudou,  Kei Yura,  Toshimichi Fujiwara,  Takeshi Kawabata,  Genji Kurisu, 
  • Pages: 173-186
  • First Published: 18 October 2021
Free Access

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D

Stephen K. Burley,  Charmi Bhikadiya,  Chunxiao Bi,  Sebastian Bittrich,  Li Chen,  Gregg V. Crichlow,  Jose M. Duarte,  Shuchismita Dutta,  Maryam Fayazi,  Zukang Feng,  Justin W. Flatt,  Sai J. Ganesan,  David S. Goodsell,  Sutapa Ghosh,  Rachel Kramer Green,  Vladimir Guranovic,  Jeremy Henry,  Brian P. Hudson,  Catherine L. Lawson,  Yuhe Liang,  Robert Lowe,  Ezra Peisach,  Irina Persikova,  Dennis W. Piehl,  Yana Rose,  Andrej Sali,  Joan Segura,  Monica Sekharan,  Chenghua Shao,  Brinda Vallat,  Maria Voigt,  John D. Westbrook,  Shamara Whetstone,  Jasmine Y. Young,  Christine Zardecki, 
  • Pages: 187-208
  • First Published: 22 October 2021
Free Access

Spatial arrangement of proteins in planar and curved membranes by PPM 3.0

Andrei L. Lomize,  Spencer C. Todd,  Irina D. Pogozheva, 
  • Pages: 209-220
  • First Published: 29 October 2021
Free Access

CHARMING: Harmonizing synonymous codon usage to replicate a desired codon usage pattern

Gabriel Wright,  Anabel Rodriguez,  Jun Li,  Tijana Milenkovic,  Scott J. Emrich,  Patricia L. Clark, 
  • Pages: 221-231
  • First Published: 04 November 2021
Open Access

DIALS as a toolkit

Graeme Winter,  James Beilsten-Edmands,  Nicholas Devenish,  Markus Gerstel,  Richard J. Gildea,  David McDonagh,  Elena Pascal,  David G. Waterman,  Benjamin H. Williams,  Gwyndaf Evans, 
  • Pages: 232-250
  • First Published: 08 November 2021
Free Access

SAXSMoW 3.0: New advances in the determination of the molecular weight of proteins in dilute solutions from SAXS intensity data on a relative scale

Mario de Oliveira Neto,  Adriano de Freitas Fernandes,  Vassili Piiadov,  Aldo Felix Craievich,  Evandro Ares de Araújo,  Igor Polikarpov, 
  • Pages: 251-258
  • First Published: 11 November 2021
Free Access

Optimal structure determination from sub-optimal diffraction data

Wladek Minor,  Marcin Cymborowski,  Dominika Borek,  David R. Cooper,  Maksymilian Chruszcz,  Zbyszek Otwinowski, 
  • Pages: 259-268
  • First Published: 15 November 2021
Open Access

EFAMIX, a tool to decompose inline chromatography SAXS data from partially overlapping components

Petr V. Konarev,  Melissa A. Graewert,  Cy M. Jeffries,  Masakazu Fukuda,  Taisiia A. Cheremnykh,  Vladimir V. Volkov,  Dmitri I. Svergun, 
  • Pages: 269-282
  • First Published: 12 November 2021
Open Access

PDBsum extras: SARS-CoV-2 and AlphaFold models

Roman A. Laskowski,  Janet M. Thornton, 
  • Pages: 283-289
  • First Published: 14 November 2021
Free Access

The importance of residue-level filtering and the Top2018 best-parts dataset of high-quality protein residues

Christopher J. Williams,  David C. Richardson,  Jane S. Richardson, 
  • Pages: 290-300
  • First Published: 14 November 2021
Open Access

Analysis of protein–ligand interactions from titrations and nuclear magnetic resonance relaxation dispersions

Emil Björklund,  Anna du Rietz,  Patrik Lundström, 
  • Pages: 301-307
  • First Published: 17 November 2021