1,758 research outputs found
Finding weakly reversible realizations of chemical reaction networks using optimization
An algorithm is given in this paper for the computation of dynamically
equivalent weakly reversible realizations with the maximal number of reactions,
for chemical reaction networks (CRNs) with mass action kinetics. The original
problem statement can be traced back at least 30 years ago. The algorithm uses
standard linear and mixed integer linear programming, and it is based on
elementary graph theory and important former results on the dense realizations
of CRNs. The proposed method is also capable of determining if no dynamically
equivalent weakly reversible structure exists for a given reaction network with
a previously fixed complex set.Comment: 18 pages, 9 figure
A maximum common substructure-based algorithm for searching and predicting drug-like compounds
Motivation: The prediction of biologically active compounds is of great importance for high-throughput screening (HTS) approaches in drug discovery and chemical genomics. Many computational methods in this area focus on measuring the structural similarities between chemical structures. However, traditional similarity measures are often too rigid or consider only global similarities between structures. The maximum common substructure (MCS) approach provides a more promising and flexible alternative for predicting bioactive compounds
Identification of target-specific bioisosteric fragments from ligand-protein crystallographic data
Bioisosteres are functional groups or atoms that are structurally different but that can form similar intermolecular interactions. Potential bioisosteres were identified here from analysing the X-ray crystallographic structures for sets of different ligands complexed with a fixed protein. The protein was used to align the ligands with each other, and then pairs of ligands compared to identify substructural features with high volume overlap that occurred in approximately the same region of geometric space. The resulting pairs of substructural features can suggest potential bioisosteric replacements for use in lead-optimisation studies. Experiments with 12 sets of ligand-protein complexes from the Protein Data Bank demonstrate the effectiveness of the procedure
Multiobjective railway alignment optimization using ballastless track and reduced cross-section in tunnel
The increasing need for railway planning and design to connect growing cities in inland mountainous areas has pushed engineering efforts toward the research of railway tracks that must comply with more restrictive constraints. In this study, a multiobjective alignment optimization (HAO), commonly used for highway projects, was carried out to identify a better solution for constructing a high-speed railway track considering technical and economic feasibilities. Then, two different and innovative scenarios were investigated: an unconventional ballastless superstructure, which is more environment-friendly than a gravel superstructure, and a reduced cross-section in a tunnel, which enables a slower design speed and then, less restrictive geometric constraints and earthmoving. The results showed that the first solution obtained a better performance with a slight increase in cost. Moreover, both scenarios improved the preliminary alignment optimization, reducing the overall cost by 11% for the first scenario and 20% for the second one
- …