A5047604622- Protein Structure and Dynamics
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Computational Drug Discovery Methods
- Scientific Computing and Data Management
- Enzyme Structure and Function
- Evolution and Genetic Dynamics
- Gene Regulatory Network Analysis
- Mass Spectrometry Techniques and Applications
- Chromosomal and Genetic Variations
- Genetic diversity and population structure
- CRISPR and Genetic Engineering
- Lipid Membrane Structure and Behavior
- RNA and protein synthesis mechanisms
- Machine Learning in Bioinformatics
Leipzig University
2021-2024
Rice University
2013-2014
Adaptation to ecologically complex environments can provide insights into the evolutionary dynamics and functional constraints encountered by organisms during natural selection. a new environment with abundant varied resources be difficult achieve small incremental changes if many mutations are required even modest gains in fitness. Since changing quite common nature, we investigated how such an epistatic bottleneck avoided allow rapid adaptation. We show that adaptive arise repeatedly...
The possible effects of mutations on stability and function a protein can only be understood in the context 3D structure. MutationExplorer webserver maps sequence changes onto structures allows users to study variation by inputting changes. As user enters variants, model evolves, estimated energy are highlighted. In addition basic per-residue input format, also upload an entire replacement sequence. Previously purview desktop applications, such back-mutate PDB wildtype single step. Another...
Phylogenomic analyses involving whole-genome or multi-locus data often entail dealing with incongruent gene trees. In this paper, we consider two causes of such incongruence, namely, incomplete lineage sorting (ILS) and hybridization, both parsimony probabilistic criteria for them. Under the assumption ILS, computing probability a tree given species is very hard problem. We present heuristic speeding up computation, demonstrate how it scales computations to sizes that are not feasible...
Protein-protein interactions (PPIs) play an essential role in a great variety of cellular processes and are therefore significant interest for the design new therapeutic compounds as well identification side effects due to unexpected binding. Here, we present ProteinPrompt, webserver that uses machine learning algorithms calculate specific, currently unknown PPIs. Our tool is designed quickly reliably predict contact propensities based on input sequence order scan large libraries potential...
A bstract The possible effects of mutations on stability and function a protein can only be understood in the context 3D structure. M utation E xplorer webserver maps sequence changes onto structures allows users to study variation by inputting changes. As user enters variants, model evolves, estimated energy are highlighted. In addition basic per-residue input format, also upload an entire replacement sequence. Previously purview desktop applications, such back-mutate PDB wildtype single...
Abstract We present an updated version of the Voronoia service that enables fully automated analysis atomic packing density macromolecules. combines previous efforts to analyse 3D protein and RNA structures into a single service, combined with state-of-the-art online visualization. uses Voronoi cell method calculate free space between neighbouring atoms estimate van der Waals interactions. Compared other methods derive interactions by calculating solvent-free surfaces, it explicitly...
The AlignMe web server is dedicated to accurately aligning sequences of membrane proteins, a particularly challenging task due the strong evolutionary divergence and low compositional complexity hydrophobic membrane-spanning proteins. can create pairwise alignments either two primary amino acid or hydropathy profiles. for has been continuously available >10 years, supporting 1000s users per year. Recent improvements include anchoring, multiple submissions, structure visualization. Anchoring...
The SmoothT software and webservice offers the construction of pathways from an ensemble conformations. user provides archive molecule conformations in Protein Databank (PDB) format, which a starting final conformation need to be selected. individual PDB files contain energy value or score, estimating quality respective confirmation. Additionally, has provide root-mean-square deviation (RMSD) cut-off, below are considered neighboring. From this, constructs graph that connects similar...
Abstract Motivation Protein-protein interactions play an essential role in a great variety of cellular processes and are therefore significant interest for the design new therapeutic compounds as well identification side-effects due to unexpected binding. Here, we present ProteinPrompt , webserver that uses machine-learning algorithms calculate specific, currently unknown protein-protein interactions. Our tool is designed quickly reliably predict contacts based on input sequence order scan...