Success: evolutionary and structural properties of amino acids prove effective for succinylation site prediction

Y López, A Sharma, A Dehzangi, SP Lal… - BMC genomics, 2018 - Springer
Background Post-translational modification is considered an important biological
mechanism with critical impact on the diversification of the proteome. Although a long list of …

SucStruct: prediction of succinylated lysine residues by using structural properties of amino acids

Y López, A Dehzangi, SP Lal, G Taherzadeh… - Analytical …, 2017 - Elsevier
Abstract Post-Translational Modification (PTM) is a biological reaction which contributes to
diversify the proteome. Despite many modifications with important roles in cellular activity …

[PDF][PDF] Proteome-wide structural analysis identifies warhead-and coverage-specific biases in cysteine-focused chemoproteomics

MEH White, J Gil, EW Tate - Cell Chemical Biology, 2023 - cell.com
Covalent drug discovery has undergone a resurgence over the past two decades and
reactive cysteine profiling has emerged in parallel as a platform for ligand discovery through …

Structure of the transcription activator target Tra1 within the chromatin modifying complex SAGA

G Sharov, K Voltz, A Durand, O Kolesnikova… - Nature …, 2017 - nature.com
The transcription co-activator complex SAGA is recruited to gene promoters by sequence-
specific transcriptional activators and by chromatin modifications to promote pre-initiation …

PhoglyStruct: Prediction of phosphoglycerylated lysine residues using structural properties of amino acids

A Chandra, A Sharma, A Dehzangi, S Ranganathan… - Scientific reports, 2018 - nature.com
The biological process known as post-translational modification (PTM) contributes to
diversifying the proteome hence affecting many aspects of normal cell biology and …

StackCBPred: A stacking based prediction of protein-carbohydrate binding sites from sequence

S Gattani, A Mishra, MT Hoque - Carbohydrate research, 2019 - Elsevier
Carbohydrate-binding proteins play vital roles in many important biological processes. The
study of these protein-carbohydrate interactions, at residue level, is useful in treating many …

GNL-Scorer: a generalized model for predicting CRISPR on-target activity by machine learning and featurization

J Wang, X Xiang, L Bolund, X Zhang… - Journal of molecular …, 2020 - academic.oup.com
We initially extracted 13 datasets from different experiments among six species: human,
mouse, zebrafish, Drosophila, Ciona intestinalis, and C. elegans (Supplementary Table 1) …

Accurately predicting mutation-caused stability changes from protein sequences using extreme gradient boosting

X Lv, J Chen, Y Lu, Z Chen, N Xiao… - Journal of chemical …, 2020 - ACS Publications
Accurately predicting the impact of point mutation on protein stability has crucial roles in
protein design and engineering. In this study, we proposed a novel method (BoostDDG) to …

Predicting lysine‐malonylation sites of proteins using sequence and predicted structural features

G Taherzadeh, Y Yang, H Xu, Y Xue… - Journal of …, 2018 - Wiley Online Library
Malonylation is a recently discovered post‐translational modification (PTM) in which a
malonyl group attaches to a lysine (K) amino acid residue of a protein. In this work, a novel …

iProtGly‐SS: Identifying protein glycation sites using sequence and structure based features

MM Islam, S Saha, MM Rahman… - Proteins: Structure …, 2018 - Wiley Online Library
Glycation is chemical reaction by which sugar molecule bonds with a protein without the
help of enzymes. This is often cause to many diseases and therefore the knowledge about …