Quantum mechanical continuum solvation models

J Tomasi, B Mennucci, R Cammi - Chemical reviews, 2005 - ACS Publications
This review on continuum solvation models has been preceded in Chemical Reviews by
others addressing the same subject. They are due to Tomasi and Persico1 (published in …

Generalized‐ensemble algorithms for molecular simulations of biopolymers

A Mitsutake, Y Sugita, Y Okamoto - Peptide Science: Original …, 2001 - Wiley Online Library
In complex systems with many degrees of freedom such as peptides and proteins, there
exists a huge number of local‐minimum‐energy states. Conventional simulations in the …

[HTML][HTML] New machine learning and physics-based scoring functions for drug discovery

IA Guedes, AMS Barreto, D Marinho, E Krempser… - Scientific reports, 2021 - nature.com
Scoring functions are essential for modern in silico drug discovery. However, the accurate
prediction of binding affinity by scoring functions remains a challenging task. The …

[图书][B] DNA replication

A Kornberg, TA Baker - 2005 - books.google.com
Often imitated but never rivalled, DNA Replication, regarded around the world as a classic of
modern science, is now back in print in a paperback edition. Tania Baker and Nobel Prize …

CRISPR–Cas9 bends and twists DNA to read its sequence

JC Cofsky, KM Soczek, GJ Knott, E Nogales… - Nature structural & …, 2022 - nature.com
In bacterial defense and genome editing applications, the CRISPR-associated protein Cas9
searches millions of DNA base pairs to locate a 20-nucleotide, guide RNA-complementary …

Theoretical methods for the description of the solvent effect in biomolecular systems

M Orozco, FJ Luque - Chemical Reviews, 2000 - ACS Publications
The environment plays a key role in the determination of the properties and reactivity of
substances in condensed phases. The complexity of chemical phenomena in solution has …

A mechanistic perspective on the chemistry of DNA repair glycosylases

JT Stivers, YL Jiang - Chemical reviews, 2003 - ACS Publications
DNA was selected over the course of evolution as the ideal molecule for coding and storing
the genetic blueprint of life. One primary driving force for selecting DNA as the repository for …

Evaluation of a fast implicit solvent model for molecular dynamics simulations

P Ferrara, J Apostolakis… - … : Structure, Function, and …, 2002 - Wiley Online Library
A solvation term based on the solvent accessible surface area (SASA) is combined with the
CHARMM polar hydrogen force field for the efficient simulation of peptides and small …

Nucleotide excision repair in Escherichia coli

B Van Houten - Microbiological reviews, 1990 - Am Soc Microbiol
One of the best-studied DNA repair pathways is nucleotide excision repair, a process
consisting of DNA damage recognition, incision, excision, repair resynthesis, and DNA …

Promoters responsive to DNA bending: a common theme in prokaryotic gene expression

J Pérez-Martín, F Rojo, V De Lorenzo - Microbiological reviews, 1994 - Am Soc Microbiol
The early notion of DNA as a passive target for regulatory proteins has given way to the
realization that higher-order DNA structures and DNA-protein complexes are at the basis of …