[HTML][HTML] Boosting the full potential of PyMOL with structural biology plugins
S Rosignoli, A Paiardini - Biomolecules, 2022 - mdpi.com
Over the past few decades, the number of available structural bioinformatics pipelines,
libraries, plugins, web resources and software has increased exponentially and become …
libraries, plugins, web resources and software has increased exponentially and become …
What is bioinformatics? A proposed definition and overview of the field
NM Luscombe, D Greenbaum… - Methods of information …, 2001 - thieme-connect.com
Background: The recent flood of data from genome sequences and functional genomics has
given rise to new field, bioinformatics, which combines elements of biology and computer …
given rise to new field, bioinformatics, which combines elements of biology and computer …
CATH: increased structural coverage of functional space
Abstract CATH (https://www. cathdb. info) identifies domains in protein structures from
wwPDB and classifies these into evolutionary superfamilies, thereby providing structural and …
wwPDB and classifies these into evolutionary superfamilies, thereby providing structural and …
[HTML][HTML] AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms
Deep-learning (DL) methods like DeepMind's AlphaFold2 (AF2) have led to substantial
improvements in protein structure prediction. We analyse confident AF2 models from 21 …
improvements in protein structure prediction. We analyse confident AF2 models from 21 …
CATH: an expanded resource to predict protein function through structure and sequence
The latest version of the CATH-Gene3D protein structure classification database has
recently been released (version 4.1, http://www. cathdb. info). The resource comprises over …
recently been released (version 4.1, http://www. cathdb. info). The resource comprises over …
T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension
This article introduces a new interface for T-Coffee, a consistency-based multiple sequence
alignment program. This interface provides an easy and intuitive access to the most popular …
alignment program. This interface provides an easy and intuitive access to the most popular …
T-Coffee: A novel method for fast and accurate multiple sequence alignment
We describe a new method (T-Coffee) for multiple sequence alignment that provides a
dramatic improvement in accuracy with a modest sacrifice in speed as compared to the most …
dramatic improvement in accuracy with a modest sacrifice in speed as compared to the most …
Contrastive learning on protein embeddings enlightens midnight zone
Experimental structures are leveraged through multiple sequence alignments, or more
generally through homology-based inference (HBI), facilitating the transfer of information …
generally through homology-based inference (HBI), facilitating the transfer of information …
[PDF][PDF] Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
E Krissinel, K Henrick - Acta Crystallographica Section D …, 2004 - journals.iucr.org
The present paper describes the SSM algorithm of protein structure comparison in three
dimensions, which includes an original procedure of matching graphs built on the protein's …
dimensions, which includes an original procedure of matching graphs built on the protein's …
Twilight zone of protein sequence alignments
B Rost - Protein engineering, 1999 - academic.oup.com
Sequence alignments unambiguously distinguish between protein pairs of similar and non-
similar structure when the pairwise sequence identity is high (> 40% for long alignments) …
similar structure when the pairwise sequence identity is high (> 40% for long alignments) …