Understanding cervical cancer through proteomics
F Martínez-Rodríguez, JE Limones-González… - Cells, 2021 - mdpi.com
Cancer is one of the leading public health issues worldwide, and the number of cancer
patients increases every day. Particularly, cervical cancer (CC) is still the second leading …
patients increases every day. Particularly, cervical cancer (CC) is still the second leading …
NAPS: network analysis of protein structures
B Chakrabarty, N Parekh - Nucleic acids research, 2016 - academic.oup.com
Traditionally, protein structures have been analysed by the secondary structure architecture
and fold arrangement. An alternative approach that has shown promise is modelling …
and fold arrangement. An alternative approach that has shown promise is modelling …
Integrated biophysical modeling of the SARS-CoV-2 spike protein binding and allosteric interactions with antibodies
GM Verkhivker, L Di Paola - The Journal of Physical Chemistry B, 2021 - ACS Publications
Structural and biochemical studies of the severe acute respiratory syndrome (SARS)-CoV-2
spike glycoproteins and complexes with highly potent antibodies have revealed multiple …
spike glycoproteins and complexes with highly potent antibodies have revealed multiple …
CMView: interactive contact map visualization and analysis
Contact maps are a valuable visualization tool in structural biology. They are a convenient
way to display proteins in two dimensions and to quickly identify structural features such as …
way to display proteins in two dimensions and to quickly identify structural features such as …
Antigen binding allosterically promotes Fc receptor recognition
J Zhao, R Nussinov, B Ma - MAbs, 2019 - Taylor & Francis
ABSTRACT A key question in immunology is whether antigen recognition and Fc receptor
(FcR) binding are allosterically linked. This question is also relevant for therapeutic antibody …
(FcR) binding are allosterically linked. This question is also relevant for therapeutic antibody …
MAPIYA contact map server for identification and visualization of molecular interactions in proteins and biological complexes
AE Badaczewska-Dawid, C Nithin… - Nucleic Acids …, 2022 - academic.oup.com
Correct identification and effective visualization of interactions in biomolecular structures
facilitate understanding of their functions and molecular design. In response to the practical …
facilitate understanding of their functions and molecular design. In response to the practical …
Mechanisms of recognition of amyloid-β (Aβ) monomer, oligomer, and fibril by homologous antibodies
J Zhao, R Nussinov, B Ma - Journal of Biological Chemistry, 2017 - ASBMB
Alzheimer's disease is one of the most devastating neurodegenerative diseases without
effective therapies. Immunotherapy is a promising approach, but amyloid antibody structural …
effective therapies. Immunotherapy is a promising approach, but amyloid antibody structural …
Toward an accurate prediction of inter-residue distances in proteins using 2D recursive neural networks
Background Protein inter-residue contact maps provide a translation and rotation invariant
topological representation of a protein. They can be used as an intermediary step in protein …
topological representation of a protein. They can be used as an intermediary step in protein …
An integrated 3-dimensional genome modeling engine for data-driven simulation of spatial genome organization
ChIA-PET is a high-throughput mapping technology that reveals long-range chromatin
interactions and provides insights into the basic principles of spatial genome organization …
interactions and provides insights into the basic principles of spatial genome organization …
GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function
Motivation: To date, only a few distinct successful approaches have been introduced to
reconstruct a protein 3D structure from a map of contacts between its amino acid residues (a …
reconstruct a protein 3D structure from a map of contacts between its amino acid residues (a …