Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases
The identification of interactions between drugs/compounds and their targets is crucial for
the development of new drugs. In vitro screening experiments (ie bioassays) are frequently …
the development of new drugs. In vitro screening experiments (ie bioassays) are frequently …
A review of methods available to estimate solvent-accessible surface areas of soluble proteins in the folded and unfolded states
S Ausaf Ali, M Imtaiyaz Hassan, A Islam… - Current Protein and …, 2014 - benthamdirect.com
Solvent accessible surface area (SASA) of proteins has always been considered as a
decisive factor in protein folding and stability studies. It is defined as the surface …
decisive factor in protein folding and stability studies. It is defined as the surface …
CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction
Y Xu, S Wang, Q Hu, S Gao, X Ma, W Zhang… - Nucleic acids …, 2018 - academic.oup.com
CavityPlus is a web server that offers protein cavity detection and various functional
analyses. Using protein three-dimensional structural information as the input, CavityPlus …
analyses. Using protein three-dimensional structural information as the input, CavityPlus …
[HTML][HTML] FreeSASA: An open source C library for solvent accessible surface area calculations
S Mitternacht - F1000Research, 2016 - ncbi.nlm.nih.gov
Calculating solvent accessible surface areas (SASA) is a run-of-the-mill calculation in
structural biology. Although there are many programs available for this calculation, there are …
structural biology. Although there are many programs available for this calculation, there are …
Multiple sequence alignment-based RNA language model and its application to structural inference
Compared with proteins, DNA and RNA are more difficult languages to interpret because
four-letter coded DNA/RNA sequences have less information content than 20-letter coded …
four-letter coded DNA/RNA sequences have less information content than 20-letter coded …
COCOMAPS: a web application to analyze and visualize contacts at the interface of biomolecular complexes
Herein we present COCOMAPS, a novel tool for analyzing, visualizing and comparing the
interface in protein–protein and protein–nucleic acids complexes. COCOMAPS combines …
interface in protein–protein and protein–nucleic acids complexes. COCOMAPS combines …
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters
Understanding the function of complex RNA molecules depends critically on understanding
their structure. However, creating three-dimensional (3D) structural models of RNA remains …
their structure. However, creating three-dimensional (3D) structural models of RNA remains …
Comparative evaluation of covalent docking tools
A Scarpino, GG Ferenczy… - Journal of Chemical …, 2018 - ACS Publications
Increased interest in covalent drug discovery led to the development of computer programs
predicting binding mode and affinity of covalent inhibitors. Here we compare the …
predicting binding mode and affinity of covalent inhibitors. Here we compare the …
Site-specific reactivity of nonenzymatic lysine acetylation
Protein acetylation of lysine ε-amino groups is abundant in cells, particularly within
mitochondria. The contribution of enzyme-catalyzed and nonenzymatic acetylation in …
mitochondria. The contribution of enzyme-catalyzed and nonenzymatic acetylation in …
Allicin induces thiol stress in bacteria through S-allylmercapto modification of protein cysteines
A Müller, J Eller, F Albrecht, P Prochnow… - Journal of Biological …, 2016 - ASBMB
Allicin (diallyl thiosulfinate) from garlic is a highly potent natural antimicrobial substance. It
inhibits growth of a variety of microorganisms, among them antibiotic-resistant strains …
inhibits growth of a variety of microorganisms, among them antibiotic-resistant strains …