Computational analysis of amino acid mutation: a proteome wide perspective

J Chen, B Shen - Current Proteomics, 2009 - ingentaconnect.com
Amino acid mutations may have diverse effects on protein structure and function. Thus
reliable information about the protein sequence variations is essential to gain insights into …

[HTML][HTML] Predicting the functional effect of amino acid substitutions and indels

Y Choi, GE Sims, S Murphy, JR Miller, AP Chan - 2012 - journals.plos.org
As next-generation sequencing projects generate massive genome-wide sequence
variation data, bioinformatics tools are being developed to provide computational …

Computational approaches to study the effects of small genomic variations

K Khafizov, MV Ivanov, OV Glazova… - Journal of molecular …, 2015 - Springer
Advances in DNA sequencing technologies have led to an avalanche-like increase in the
number of gene sequences deposited in public databases over the last decade as well as …

[HTML][HTML] Correlated mutations: a hallmark of phenotypic amino acid substitutions

A Kowarsch, A Fuchs, D Frishman… - PLoS computational …, 2010 - journals.plos.org
Point mutations resulting in the substitution of a single amino acid can cause severe
functional consequences, but can also be completely harmless. Understanding what …

[HTML][HTML] Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset

TAP de Beer, RA Laskowski, SL Parks… - PLoS computational …, 2013 - journals.plos.org
The 1000 Genomes Project data provides a natural background dataset for amino acid
germline mutations in humans. Since the direction of mutation is known, the amino acid …

[HTML][HTML] Comparative analysis of web-based programs for single amino acid substitutions in proteins

A Choudhury, T Mohammad, F Anjum, A Shafie… - PloS one, 2022 - journals.plos.org
Single amino-acid substitution in a protein affects its structure and function. These changes
are the primary reasons for the advent of many complex diseases. Analyzing single point …

Prediction of pathological mutations in proteins: the challenge of integrating sequence conservation and structure stability principles

C Riera, S Lois, X de la Cruz - Wiley Interdisciplinary Reviews …, 2014 - Wiley Online Library
The recent drop in genome sequencing costs has created a promising horizon for the
development of genomic medicine. Within the biomedical environment, sequencing data are …

[HTML][HTML] The loss and gain of functional amino acid residues is a common mechanism causing human inherited disease

J Lugo-Martinez, V Pejaver, KA Pagel… - PLoS computational …, 2016 - journals.plos.org
Elucidating the precise molecular events altered by disease-causing genetic variants
represents a major challenge in translational bioinformatics. To this end, many studies have …

Annotating mutational effects on proteins and protein interactions: designing novel and revisiting existing protocols

M Li, A Goncearenco, AR Panchenko - Proteomics: Methods and …, 2017 - Springer
In this review we describe a protocol to annotate the effects of missense mutations on
proteins, their functions, stability, and binding. For this purpose we present a collection of the …

Use of estimated evolutionary strength at the codon level improves the prediction of disease‐related protein mutations in humans

E Capriotti, L Arbiza, R Casadio, J Dopazo… - Human …, 2008 - Wiley Online Library
Predicting the functional impact of protein variation is one of the most challenging problems
in bioinformatics. A rapidly growing number of genome‐scale studies provide large amounts …