Protein sequence alignment is a key component of most bioinformatics pipelines to study the structures and functions of proteins. Aligning highly divergent sequences remains, however, a difficult task that current algorithms often fail to perform accurat
Protein sequence threading, the alignment problem, and a two-step strategy - Huber, Torda - 1999Huber, T. Torda, AE, Protein sequence threading, the alignment problem and a two step strategy. J Comput Chem 1999;20:1455-1467.Huber T, Torda AE: Protein sequence threading, the alignmen...
While sequence alignments are accurate for proteins of high sequence similarity, they become unreliable as they approach the so-called 'twilight zone' where sequence similarity gets indistinguishable from random. For such distant pairs, structure alignment is of much better quality. Nevertheless, ...
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat. Methods 9, 173–175 (2012). Article Google Scholar Johnson, L. S., Eddy, S. R. & Portugaly, E. Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinform. 11, 431 (2010)...
We propose a Bayesian method to align proteins usingboth the sequence and 3-D structure of the proteins. The problem involves whatare known as "gaps" in the sequence, which we incorporate in our model, and anMCMC implementation is provided. Also, we show that the procedure can be usedto ...
Homology-based methods need templates with known domain annotations and efficient sequence alignment algorithms to find templates that match a target sequence. For example, CHOP [6] implements three hierarchical steps to predict domain boundaries. Target sequences are aligned with data from PDB [7],...
3C). The model designs are more variable in solvent-exposed regions, akin to sequences homologous to the native structure found through multiple sequence alignment (MSA) (Fig. 2E). Furthermore, the secondary structure prediction accuracy for model-designed sequences are comparable to that of the...
Kumar and Gromiha (2006) developed the Protein-protein Interactions Thermodynamic Database (PINT), which contains several thermodynamic parameters along with sequence and structural information, experimental conditions, and literature information. Each entry contains numerical data for the free energy change...
Zhang, C., Zheng, W., Mortuza, S., Li, Y. & Zhang, Y. DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins.Bioinformatics36, 2105–2112 (2020). ArticleGoogle Scholar ...
An MSA is a matrix\({{{\mathcal{M}}}\)withLcolumns, representing the different amino-acid sites, andMrows. Each rowi, denoted byx(i), represents one sequence of the alignment. We will refer toLas the MSA length, and toMas its depth. For all but one (PF13354) of our full MSAs,...