Universal QM/MM approaches for general nanoscale applications
Quantum mechanics/molecular mechanics (QM/MM) hybrid models allow one to address
chemical phenomena in complex molecular environments. Whereas this modeling approach …
chemical phenomena in complex molecular environments. Whereas this modeling approach …
Advancements in small molecule drug design: A structural perspective
In this review, we outline recent advancements in small molecule drug design from a
structural perspective. We compare protein structure prediction methods and explore the …
structural perspective. We compare protein structure prediction methods and explore the …
AmberTools
AmberTools | Journal of Chemical Information and Modeling ACS ACS Publications C&EN CAS
Find my institution Log In Journal of Chemical Information and Modeling ACS Publications …
Find my institution Log In Journal of Chemical Information and Modeling ACS Publications …
Quantum mechanics/molecular mechanics simulations on NVIDIA and AMD graphics processing units
We have ported and optimized the graphics processing unit (GPU)-accelerated QUICK and
AMBER-based ab initio quantum mechanics/molecular mechanics (QM/MM) implementation …
AMBER-based ab initio quantum mechanics/molecular mechanics (QM/MM) implementation …
The application of QM/MM simulations in heterogeneous catalysis
GA Bramley, OT Beynon, PV Stishenko… - Physical Chemistry …, 2023 - pubs.rsc.org
The QM/MM simulation method is provenly efficient for the simulation of biological systems,
where an interplay of extensive environment and delicate local interactions drives a process …
where an interplay of extensive environment and delicate local interactions drives a process …
Best practices on QM/MM simulations of biological systems
CM Clemente, L Capece, MA Martí - Journal of Chemical …, 2023 - ACS Publications
During the second half of the 20th century, following structural biology hallmark works on
DNA and proteins, biochemists shifted their questions from “what does this molecule look …
DNA and proteins, biochemists shifted their questions from “what does this molecule look …
Computer-aided drug design, quantum-mechanical methods for biological problems
Quantum chemistry enables to study systems with chemical accuracy (< 1 kcal/mol from
experiment) but is restricted to a handful of atoms due to its computational expense. This has …
experiment) but is restricted to a handful of atoms due to its computational expense. This has …
[HTML][HTML] An understanding of coronavirus and exploring the molecular dynamics simulations to find promising candidates against the Mpro of nCoV to combat the …
The first infection case of new coronavirus was reported at the end of 2019 and after then,
the cases are reported in all nations across the world in a very short period. Further, the …
the cases are reported in all nations across the world in a very short period. Further, the …
Role of enzyme and active site conformational dynamics in the catalysis by α-amylase explored with QM/MM molecular dynamics
RPP Neves, PA Fernandes… - Journal of Chemical …, 2022 - ACS Publications
We assessed enzyme: substrate conformational dynamics and the rate-limiting glycosylation
step of a human pancreatic α-amylase: maltopentose complex. Microsecond molecular …
step of a human pancreatic α-amylase: maltopentose complex. Microsecond molecular …
Designing drugs when there is low data availability: one-shot learning and other approaches to face the issues of a long-term concern
GC Verissimo, MSM Serafim… - Expert Opinion on …, 2022 - Taylor & Francis
Introduction Modern drug discovery is generally accessed by useful information from
previous large databases or uncovering novel data. The lack of biological and/or chemical …
previous large databases or uncovering novel data. The lack of biological and/or chemical …