Is it reliable to use common molecular docking methods for comparing the binding affinities of enantiomer pairs for their protein target?
D Ramírez, J Caballero - International journal of molecular sciences, 2016 - mdpi.com
Molecular docking is a computational chemistry method which has become essential for the
rational drug design process. In this context, it has had great impact as a successful tool for …
rational drug design process. In this context, it has had great impact as a successful tool for …
FAM111A protects replication forks from protein obstacles via its trypsin-like domain
Y Kojima, Y Machida, S Palani, TR Caulfield… - Nature …, 2020 - nature.com
Persistent protein obstacles on genomic DNA, such as DNA-protein crosslinks (DPCs) and
tight nucleoprotein complexes, can block replication forks. DPCs can be removed by the …
tight nucleoprotein complexes, can block replication forks. DPCs can be removed by the …
Low‐barrier and canonical hydrogen bonds modulate activity and specificity of a catalytic triad
P Kumar, PK Agarwal, MB Waddell, T Mittag… - Angewandte …, 2019 - Wiley Online Library
The position, bonding and dynamics of hydrogen atoms in the catalytic centers of proteins
are essential for catalysis. The role of short hydrogen bonds in catalysis has remained highly …
are essential for catalysis. The role of short hydrogen bonds in catalysis has remained highly …
DelPhi suite: new developments and review of functionalities
Electrostatic potential, energies, and forces affect virtually any process in molecular biology,
however, computing these quantities is a difficult task due to irregularly shaped …
however, computing these quantities is a difficult task due to irregularly shaped …
A low-barrier hydrogen bond mediates antibiotic resistance in a noncanonical catalytic triad
P Kumar, EH Serpersu, MJ Cuneo - Science advances, 2018 - science.org
One group of enzymes that confer resistance to aminoglycoside antibiotics through covalent
modification belongs to the GCN5-related N-acetyltransferase (GNAT) superfamily. We show …
modification belongs to the GCN5-related N-acetyltransferase (GNAT) superfamily. We show …
The Se–S bond formation in the covalent inhibition mechanism of SARS-CoV-2 main protease by Ebselen-like inhibitors: a computational study
The inhibition mechanism of the main protease (Mpro) of SARS-CoV-2 by ebselen (EBS)
and its analog with a hydroxyl group at position 2 of the benzisoselenazol-3 (2H)-one ring …
and its analog with a hydroxyl group at position 2 of the benzisoselenazol-3 (2H)-one ring …
Attacking COVID-19 progression using multi-drug therapy for synergetic target engagement
COVID-19 is a devastating respiratory and inflammatory illness caused by a new
coronavirus that is rapidly spreading throughout the human population. Over the past 12 …
coronavirus that is rapidly spreading throughout the human population. Over the past 12 …
Protein-protein binding as a two-step mechanism: Preselection of encounter poses during the binding of BPTI and trypsin
Biomolecular recognition between proteins follows complex mechanisms, the understanding
of which can substantially advance drug discovery efforts. Here, we track each step of the …
of which can substantially advance drug discovery efforts. Here, we track each step of the …
Electrostatic attraction of weak monoacid anions increases probability for protonation and passage through aquaporins
M Rothert, D Rönfeldt, E Beitz - Journal of Biological Chemistry, 2017 - ASBMB
A positive electrostatic field emanating from the center of the aquaporin (AQP) water and
solute channel is responsible for the repulsion of cations. At the same time, however, a …
solute channel is responsible for the repulsion of cations. At the same time, however, a …
Docking, interaction fingerprint, and three-dimensional quantitative structure–activity relationship (3D-QSAR) of Sigma1 receptor ligands, analogs of the …
JL Velázquez-Libera, G Rossino… - Frontiers in …, 2019 - frontiersin.org
The human Sigma1 receptor (S1R), which has been identified as a target with an important
role in neuropsychological disorders, was first crystallized 3 years ago. Since S1R structure …
role in neuropsychological disorders, was first crystallized 3 years ago. Since S1R structure …