Critical assessment of methods for predicting the 3D structure of proteins and protein complexes
SJ Wodak, S Vajda, MF Lensink… - Annual review of …, 2023 - annualreviews.org
Advances in a scientific discipline are often measured by small, incremental steps. In this
review, we report on two intertwined disciplines in the protein structure prediction field …
review, we report on two intertwined disciplines in the protein structure prediction field …
Affinity maturation of antibody fragments: A review encompassing the development from random approaches to computational rational optimization
J Li, G Kang, J Wang, H Yuan, Y Wu, S Meng… - International journal of …, 2023 - Elsevier
Routinely screened antibody fragments usually require further in vitro maturation to achieve
the desired biophysical properties. Blind in vitro strategies can produce improved ligands by …
the desired biophysical properties. Blind in vitro strategies can produce improved ligands by …
Diffdock-pp: Rigid protein-protein docking with diffusion models
Understanding how proteins structurally interact is crucial to modern biology, with
applications in drug discovery and protein design. Recent machine learning methods have …
applications in drug discovery and protein design. Recent machine learning methods have …
Identification of potential mutational hotspots in serratiopeptidase to address its poor pH tolerance issue
A Dhiman, R Purohit - Journal of Biomolecular Structure and …, 2023 - Taylor & Francis
Serratiopeptidase is the multifunctionality metalloendopeptidase extensively employed in
biopharmaceutical and industrial biotechnology. Despite its poor pH tolerance …
biopharmaceutical and industrial biotechnology. Despite its poor pH tolerance …
[HTML][HTML] Visual dynamics: a web application for molecular dynamics simulation using GROMACS
IHP Vieira, EB Botelho, TJ de Souza Gomes, R Kist… - BMC …, 2023 - Springer
Background The molecular dynamics is an approach to obtain kinetic and thermodynamic
characteristics of biomolecular structures. The molecular dynamics simulation softwares are …
characteristics of biomolecular structures. The molecular dynamics simulation softwares are …
[HTML][HTML] Design and prediction of aptamers assisted by in silico methods
SJ Lee, J Cho, BH Lee, D Hwang, JW Park - Biomedicines, 2023 - mdpi.com
An aptamer is a single-stranded DNA or RNA that binds to a specific target with high binding
affinity. Aptamers are developed through the process of systematic evolution of ligands by …
affinity. Aptamers are developed through the process of systematic evolution of ligands by …
[HTML][HTML] An immunoinformatic approach to assessing the immunogenic capacity of alpha-neurotoxins in elapid snake venoms
Introduction: Most elapid snakes produce venoms that contain alpha-neurotoxins (α-NTXs),
which are proteins that cause post-synaptic blockade and paralysis in snakebite …
which are proteins that cause post-synaptic blockade and paralysis in snakebite …
Nuclear localization of STING1 competes with canonical signaling to activate AHR for commensal and intestinal homeostasis
Extensive studies demonstrate the importance of the STING1 (also known as STING) protein
as a signaling hub that coordinates immune and autophagic responses to ectopic DNA in …
as a signaling hub that coordinates immune and autophagic responses to ectopic DNA in …
In silico study of SARS‐CoV‐2 spike protein RBD and human ACE‐2 affinity dynamics across variants and Omicron subvariants
S Abeywardhana, M Premathilaka… - Journal of Medical …, 2023 - Wiley Online Library
The coronavirus disease 2019 virus outbreak continues worldwide, with many variants
emerging, some of which are considered variants of concern (VOCs). The WHO designated …
emerging, some of which are considered variants of concern (VOCs). The WHO designated …
Interaction of the Inhibitory Peptides ShK and HmK with the Voltage-Gated Potassium Channel KV1.3: Role of Conformational Dynamics
Peptide toxins that adopt the ShK fold can inhibit the voltage-gated potassium channel KV1.
3 with IC50 values in the pM range and are therefore potential leads for drugs targeting …
3 with IC50 values in the pM range and are therefore potential leads for drugs targeting …