Daniel R Roe
Overview
Explore the profile of Daniel R Roe including associated specialties, affiliations and a list of published articles.
Author names and details appear as published. Due to indexing inconsistencies, multiple individuals may share a name, and a single author may have variations. MedLuna displays this data as publicly available, without modification or verification
Snapshot
Snapshot
Articles
33
Citations
3656
Followers
0
Related Specialties
Related Specialties
Top 10 Co-Authors
Top 10 Co-Authors
Published In
Affiliations
Affiliations
Soon will be listed here.
Recent Articles
1.
Chen L, Roe D, Alain Miranda-Quintana R
bioRxiv
. 2025 Mar;
PMID: 40060588
Unsupervised learning techniques play a pivotal role in unraveling protein folding landscapes, constructing Markov State Models, expediting replica exchange simulations, and discerning drug binding patterns, among other applications. A fundamental...
2.
Chen L, Smith M, Roe D, Alain Miranda-Quintana R
bioRxiv
. 2024 Dec;
PMID: 39677679
We are transforming Radial Threshold Clustering (RTC), an algorithm, into Extended Quality Clustering, an algorithm with several novel features. Daura et al's RTC algorithm is a partitioning clustering algorithm that...
3.
Love O, Galindo-Murillo R, Roe D, Dans P, Cheatham Iii T, Bergonzo C
J Chem Theory Comput
. 2024 Oct;
20(21):9354-9363.
PMID: 39468889
Modified nucleic acids have surged as a popular therapeutic route, emphasizing the importance of nucleic acid research in drug discovery and development. Beyond well-known RNA vaccines, antisense oligonucleotides and aptamers...
4.
Hwang W, Austin S, Blondel A, Boittier E, Boresch S, Buck M, et al.
J Phys Chem B
. 2024 Sep;
128(41):9976-10042.
PMID: 39303207
Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in...
5.
Chen L, Roe D, Kochert M, Simmerling C, Alain Miranda-Quintana R
J Chem Theory Comput
. 2024 Jun;
20(13):5583-5597.
PMID: 38905589
One of the key challenges of -means clustering is the seed selection or the initial centroid estimation since the clustering result depends heavily on this choice. Alternatives such as -means++...
6.
Chen L, Roe D, Kochert M, Simmerling C, Alain Miranda-Quintana R
bioRxiv
. 2024 Mar;
PMID: 38496504
One of the key challenges of -means clustering is the seed selection or the initial centroid estimation since the clustering result depends heavily on this choice. Alternatives such as -means++...
7.
Roe D, Brooks B
J Comput Chem
. 2023 Dec;
45(10):633-637.
PMID: 38071482
The grid inhomogeneous solvation theory (GIST) method requires the often time-consuming calculation of water-water and water-solute energy on a grid. Previous efforts to speed up this calculation include using OpenMP,...
8.
Case D, Aktulga H, Belfon K, Cerutti D, Cisneros G, Cruzeiro V, et al.
J Chem Inf Model
. 2023 Oct;
63(20):6183-6191.
PMID: 37805934
AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within AmberTools23 are briefly described in this Application...
9.
Roe D, Brooks B
Protein Sci
. 2022 Nov;
31(12):e4511.
PMID: 36382864
Molecular dynamics (MD) simulations are now able to routinely reach timescales of microseconds and beyond. This has led to a corresponding increase in the amount of MD trajectory data that...
10.
Roe D, Bergonzo C
J Comput Chem
. 2022 Mar;
43(13):930-935.
PMID: 35318701
Setting up molecular dynamics simulations from experimentally determined structures is often complicated by a variety of factors, particularly the inclusion of carbohydrates, since these have several anomer types which can...