Search · four archives
Search · four archives
24 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…
S. Young, Jérôme Gilles
A 3D chaos game is shown to be a useful way for encoding DNA sequences. Since matching subsequences in DNA converge in space in 3D chaos game encoding, a DNA sequence's 3D chaos game representation can be used to compare DNA sequences without prior alignment and without truncating or padding any of the sequences. Two…
Michael Himpel, A. Melzer
The temperature of a dust ensemble in a dusty plasma is one of its most fundamental properties. Here, we present experiments using the configurational temperature as a tool for the temperature analysis in dusty plasmas. Using a model of the particle interactions, the configurational temperature allows us to determine…
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…
S. Srivastava, S. B. Lal, D. C. Mishra, U. B. Angadi + 3 more
Comparison of protein structures is an important for understanding structural, functional and evolutionary relationship among protein specially in case of novel proteins . In addition to this, it is being extensively used for identifying homologous residues , finding recurrent folds , identifying structural motifs and…
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…
Juliana Alves Pereira, Mathieu Acher, Hugo Martin, Jean-Marc Jézéquel + 2 more
'Jean-Marc Jézéquel' 'Goetz Botterweck' 'Anthony Ventresque'] JULIANA ALVES PEREIRA, Univ Rennes, Inria, CNRS, IRISA, France HUGO MARTIN, Univ Rennes, Inria, CNRS, IRISA, France MATHIEU ACHER, Univ Rennes, Inria, CNRS, IRISA, France JEAN-MARC JÉZÉQUEL, Univ Rennes, Inria, CNRS, IRISA, France GOETZ BOTTERWECK…
Stefan Vuckovic
Nearly all electronic structure simulations begin with obtaining approximate geometries, making a systematic quantification of errors in approximate molecular structures of key importance. Recently, the geometric energy offset (GEO) framework based on a single and natural measure for quantifying and analysing these…
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…
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…
Andrzej Zielezinski, Hani Z. Girgis, Guillaume Bernard, Chris-Andre Leimeister + 15 more
Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment. Here, we present a community resource…
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.…
Luca Franco, Matteo Migliarini, Matteo Tommaso Ungaro, Egnald Çela + 5 more
Accurate evaluation of genome assemblies within highly repetitive regions, such as centromeres, remains a major open challenge in genomics. Conventional benchmarking relies on sequence alignment, which becomes problematic in regions of high homogeneity and divergence. Here, we framed centromere assembly evaluation as a…
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…
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)…
Michael Höhl, Isidore Rigoutsos, Mark A. Ragan
We have developed an alignment-free method that calculates phylogenetic distances using a maximum-likelihood approach for a model of sequence change on patterns that are discovered in unaligned sequences. To evaluate the phylogenetic accuracy of our method, and to conduct a comprehensive comparison of existing…
Max A Alekseyev, Pavel A Pevzner, Daniel Huson
In a landmark paper, Nadeau and Taylor [18] formulated the random breakage model (RBM) of chromosome evolution that postulates that there are no rearrangement hotspots in the human genome. In the next two decades, numerous studies with progressively increasing levels of resolution made RBM the de facto theory of…