[HTML][HTML] Principles and overview of sampling methods for modeling macromolecular structure and dynamics

T Maximova, R Moffatt, B Ma, R Nussinov… - PLoS computational …, 2016 - journals.plos.org
Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …

Computational structure modeling for diverse categories of macromolecular interactions

T Aderinwale, CW Christoffer, D Sarkar… - Current opinion in …, 2020 - Elsevier
Computational protein–protein docking is one of the most intensively studied topics in
structural bioinformatics. The field has made substantial progress through over three …

[HTML][HTML] Molecular modeling applied to nucleic acid-based molecule development

A Krüger, FM Zimbres, T Kronenberger, C Wrenger - Biomolecules, 2018 - mdpi.com
Molecular modeling by means of docking and molecular dynamics (MD) has become an
integral part of early drug discovery projects, enabling the screening and enrichment of large …

Combining H/D exchange mass spectrometry and computational docking to derive the structure of protein–protein complexes

VA Roberts, ME Pique, S Hsu, S Li - Biochemistry, 2017 - ACS Publications
Protein–protein interactions are essential for biological function, but structures of protein–
protein complexes are difficult to obtain experimentally. To derive the protein complex of the …

[PDF][PDF] A human transcription factor in search mode

K Hauser, B Essuman, E Coutsias, M Garcia-Diaz… - Biophysical …, 2015 - cell.com
Transcription factors (TF) change shape to search and recognize DNA, shifting the energy
landscape from a weak binding mode to a tight binding mode. But the mechanism of TF …

RNA–LIM: A novel procedure for analyzing protein/single-stranded RNA propensity data with concomitant estimation of interface structure

D Hall, S Li, K Yamashita, R Azuma, JA Carver… - Analytical …, 2015 - Elsevier
RNA–LIM is a procedure that can analyze various pseudo-potentials describing the affinity
between single-stranded RNA (ssRNA) ribonucleotides and surface amino acids to produce …

Advances in human biology: combining genetics and molecular biophysics to pave the way for personalized diagnostics and medicine

E Alexov - Advances in Biology, 2014 - Wiley Online Library
Advances in several biology‐oriented initiatives such as genome sequencing and structural
genomics, along with the progress made through traditional biological and biochemical …

A fragment-based docking simulation for investigating peptide–protein bindings

J Liao, YT Wang, CS Lin - Physical Chemistry Chemical Physics, 2017 - pubs.rsc.org
A fragment-based method was developed to investigate the binding conformations of
peptide ligands. This method efficiently avoids the high degree of freedom (DOF) of peptide …

[PDF][PDF] Molecular interactions of nicotine and the nitrogenous bases of DNA and RNA calculated by improved quantum methods

M González-Pérez, M Briteño-Vázquez… - World Journal of …, 2016 - academia.edu
WORLD JOURNAL OF PHARMACEUTICAL RESEARCH Page 1 www.wjpr.net Vol 5, Issue 3,
2016. 1778 M. González-Pérez et al. World Journal of Pharmaceutical Research MOLECULAR …

[PDF][PDF] Interactions analysis of four chemotherapeutic drugs vs. nitrogenous bases of DNA and RNA, using quantum methods

M González-Perez - World Journal of Pharmaceutical Research, 2016 - researchgate.net
ABSTRACT Cyclophosphamide (CPA), Melphalan (MPH) Chlorambucil (CHB) and,
Ifosfamide (IPA) are commonly used in Chemotherapy. In this research, it studied the ECTs …