Search · four archives
Search · four archives
19 papers · ranked by Valyu relevance
Authors not listed
Accurately predicting the diverse bound-state conformations of small molecules is crucial for successful drug discovery and design, particularly when detailed protein-ligand interactions are unknown. Established tools exist, but efficiently exploring the vast conformational space remains challenging. This work…
Yosef Knattrup, Jakub Kubečka, Haide Wu, Frank Jensen + 1 more
Atmospheric molecular clusters, the onset of secondary aerosol formation, are a ma- jor part of the current uncertainty in modern climate models. Quantum chemical (QC) methods are usually employed in a funneling approach to identify the lowest free energy cluster structures. However, the funneling approach highly…
Authors not listed
We present a new method for fingerprint- ing atomic configurations relevant to ML-IAM training and application, utilizing the ChIMES descriptor. These fingerprints enable rigor- ous analysis of statistical distinguishability be- tween configurations. Sample applications in- clude assessing diversity within ML-IAP…
Vamika Longia, Navdeep Singh Dhindsa, Anosh Joseph
- Department of Physical Sciences, Indian Institute of Science Education and Research Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India - Department of Theoretical Physics, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India - National Institute for Theoretical and…
Andreas Buchgraitz Jensen, Jonas Elm
Atmospheric molecular clusters are important for the formation of new aerosol particles in the air. However, current experimental techniques are not able to yield direct insight into the cluster geometries. This implies that to date there is limited information about how accurately the applied computational methods…
Authors not listed
We present a gridless framework for computing high-dimensional conformational free energy surfaces (FES) of flexible molecules using enhanced sampling trajectories. By combining concurrent well-tempered metadynamics with Density Peaks Advanced (DPA) clustering, our approach bypasses the dimensionality limitations of…
Bigoni, Davide, Bosi, Federico + 4 more
> Abstract. The discovery of configurational forces acting on elastic structures and its initial applications are reviewed. Configurational forces are related to the possibility that an elastic structure can change its configuration, thus inducing a variation in the potential energy. This concept has already led to…
Yichi Zhang, Muskaan Jindal, Shruthi Viswanath, Meera Sitharam
The structures of protein complexes allow us to understand and modulate the biological functions of the proteins. Integrative docking is a computational method to obtain the structures of a protein complex, given the atomic structures of the constituent proteins along with other experimental data on the complex, such…
Benjamin Ries, Irfan Alibay, David W H Swenson, Hannah M Baumann + 3 more
Relative binding free energy (RBFE) calculations have emerged as a powerful tool supporting ligand optimization in drug discovery. Despite many successes, the use of RBFEs can often be limited by automation problems, in particular the setup of such calculations. Atom mapping algorithms are an essential component in…
Josep Gregori
The study of viral quasispecies structure and diversity presents unique challenges in comparing samples, particularly when dealing with single experimental samples from different time points or conditions. Traditional statistical methods are often inapplicable in these scenarios, necessitating the use of resampling…
Ketrin Gjoni, Laura M. Gunsalus, Shuzhen Kuang, Evonne McArthur + 3 more
'Maureen Pittman' 'John A. Capra' 'Katherine S. Pollard'] Comparing chromatin contact maps is an essential step in quantifying how three-dimensional (3D) genome organization shapes development, evolution, and disease. However, methods often disagree, and no gold standard exists for comparing pairs of maps. Here, we…
Faisal Suwayyid, Yuta Hozumi, Hongsong Feng, Mushal Zia + 2 more
Despite the availability of various sequence analysis models, comparative genomic analysis remains a challenge in genomics, genetics, and phylogenetics. Commutative algebra, a fundamental tool in algebraic geometry and number theory, has rarely been used in data and biological sciences. In this study, we introduce…
Muhammad Arslan Shaukat, Thanh Thi Nguyen, Edbert B. Hsu, Samuel Yang + 1 more
'Samuel Yang' 'Asim Bhatti'] The emergence of viruses and their variants has made virus taxonomy more important than ever before in controlling the spread of diseases. The creation of efficient treatments and cures that target particular virus properties can be aided by understanding virus taxonomy. Alignment-based…
Ashwini V. Mohan, Anjali Goswami, Jeffrey W. Streicher
Chromosomal architecture has played a key role in the evolution of biodiversity. Detecting structural variants (SVs) on chromosomes has informed the study of speciation, sex determination, adaptation, and some of the earliest divergences in the tree of life. Here we present a computationally non-intensive approach…
Suwayyid, Faisal, Hozumi, Yuta + 8 more
Faisal Suwayyid 1 , 2 , Yuta Hozumi ∗ 2 , Hongsong Feng 3 , Mushal Zia 2 , JunJie Wee 2 , and Guo-Wei Wei†2,4, 5 1 Department of Mathematics, King Fahd University of Petroleum and Minerals, Dhahran 31261, KSA. 2 Department of Mathematics, Michigan State University, MI 48824, USA. 3 Department of Mathematics and…
Alan Yue Yang Teo, Matthieu Gautier, Laurent Brock, Jennifer Y. J. Tsai + 9 more
We introduce Vespucci, a machine-learning method to identify perturbation-responsive regions, genes and gene programs within comparative spatial transcriptomics atlases. We validate Vespucci on simulated and published datasets and show that it outperforms 19 published computational methods for spatial transcriptomics.…
Saeedeh Akbari Rokn Abadi, Melika Honarmand, Ali Hajialinaghi, Somayyeh Koohi
'Somayyeh Koohi'] Background and objective: Sequence comparison is essential in bioinformatics, serving various purposes such as taxonomy, functional inference, and drug discovery. The traditional method of aligning sequences for comparison is time-consuming, especially with large datasets. To overcome this…
Kabir Bindawa Abdullahi
This paper introduces “Kabirian-based optinalysis (KBO),” a pioneering framework that addresses the longstanding challenges in estimating symmetry/asymmetry, similarity/dissimilarity, and identity/unidentity within mathematical structures and biological sequences. The existing methods often lack a strong theoretical…
Dorota Bielińska-Wąż, Piotr Wąż, Anna Lass, Jacek Karamon + 1 more
'Koichiro Tamura'] The 4D-Dynamic Representation of DNA/RNA Sequences, an alignment-free bioinformatics method recently developed by us, has been used to study the genetic diversity of Echinococcus multilocularis in red foxes in Poland. Sequences of three mitochondrial genes, i.e., NADH dehydrogenase subunit 2 (nad2)…