Using PyMOL as a platform for computational drug design

S Yuan, HCS Chan, Z Hu - Wiley Interdisciplinary Reviews …, 2017 - Wiley Online Library
PyMOL, a cross‐platform molecular graphics tool, has been widely used for three‐
dimensional (3D) visualization of proteins, nucleic acids, small molecules, electron …

[HTML][HTML] Engineering enzyme access tunnels

P Kokkonen, D Bednar, G Pinto, Z Prokop… - Biotechnology …, 2019 - Elsevier
Enzymes are efficient and specific catalysts for many essential reactions in biotechnological
and pharmaceutical industries. Many times, the natural enzymes do not display the catalytic …

Inhibitors of bacterial H2S biogenesis targeting antibiotic resistance and tolerance

K Shatalin, A Nuthanakanti, A Kaushik, D Shishov… - Science, 2021 - science.org
Emergent resistance to all clinical antibiotics calls for the next generation of therapeutics.
Here we report an effective antimicrobial strategy targeting the bacterial hydrogen sulfide …

PDBsum: Structural summaries of PDB entries

RA Laskowski, J Jabłońska, L Pravda… - Protein …, 2018 - Wiley Online Library
PDBsum is a web server providing structural information on the entries in the Protein Data
Bank (PDB). The analyses are primarily image‐based and include protein secondary …

Structures of the TMC-1 complex illuminate mechanosensory transduction

H Jeong, S Clark, A Goehring… - Nature, 2022 - nature.com
The initial step in the sensory transduction pathway underpinning hearing and balance in
mammals involves the conversion of force into the gating of a mechanosensory transduction …

A Novel Polyester Hydrolase From the Marine Bacterium Pseudomonas aestusnigri – Structural and Functional Insights

A Bollinger, S Thies, E Knieps-Grünhagen… - Frontiers in …, 2020 - frontiersin.org
Biodegradation of synthetic polymers, in particular polyethylene terephthalate (PET), is of
great importance, since environmental pollution with PET and other plastics has become a …

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update)

L Pravda, D Sehnal, D Toušek… - Nucleic acids …, 2018 - academic.oup.com
MOLEonline is an interactive, web-based application for the detection and characterization
of channels (pores and tunnels) within biomacromolecular structures. The updated version …

Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport

J Stourac, O Vavra, P Kokkonen, J Filipovic… - Nucleic acids …, 2019 - academic.oup.com
Caver Web 1.0 is a web server for comprehensive analysis of protein tunnels and channels,
and study of the ligands' transport through these transport pathways. Caver Web is the first …

PDBsum additions

TAP De Beer, K Berka, JM Thornton… - Nucleic acids …, 2014 - academic.oup.com
Abstract PDBsum, http://www. ebi. ac. uk/pdbsum, is a website providing numerous pictorial
analyses of each entry in the Protein Data Bank. It portrays the structural features of all …

Role of distal sites in enzyme engineering

J Gu, Y Xu, Y Nie - Biotechnology Advances, 2023 - Elsevier
The limitations associated with natural enzyme catalysis have triggered the rise of the field of
protein engineering. Traditional rational design was based on the analysis of protein …