DOPE, or Discrete Optimized Protein Energy, is a statistical potential used to assess homology models in protein structure prediction. DOPE is based on...

a phospholipid Discrete optimized protein energy, a method of assessing homology models in protein structure prediction Dopamine, also...

also termed inverse folding. Protein design is then an optimization problem: using some scoring criteria, an optimized sequence that will fold to the...

for protein structure prediction, but also for modelling the protein folding pathway. Scoring functions for docking Discrete optimized protein energy CASP...

Lattice proteins are highly simplified models of protein-like heteropolymer chains on lattice conformational space which are used to investigate protein folding...

evolved proteins have optimized their folding energy landscapes, and that nature has chosen amino acid sequences so that the folded state of the protein is...

information: A well-defined finite set of discrete independent variables A precomputed numerical value (considered the "energy") associated with each element in...

Typical examples of global optimization applications include: Protein structure prediction (minimize the energy/free energy function) Computational phylogenetics...

atomic analogs. Some of the major driving forces behind protein adsorption include: surface energy, intermolecular forces, hydrophobicity, and ionic or electrostatic...

biological macromolecules. Protein–protein complexes are the most commonly attempted targets of such modelling, followed by protein–nucleic acid complexes...

attempt to mimic protein folding or apply some stochastic method to search possible solutions (i.e., global optimization of a suitable energy function). These...

efficient and accurate models. Proteins can adopt an exponential number of states when modeled discretely. Typically, a protein's conformations are represented...

and standard deviations of the discrete conformations (known as rotamers) of the amino acid side chains in proteins as a function of the backbone dihedral...

countably infinite sequence, in which the chain moves state at discrete time steps, gives a discrete-time Markov chain (DTMC). A continuous-time process is called...

codes Discrete element method Discrete optimized protein energy Discrete spectrum (physics) Discrete symmetry Disgregation Disorder operator Dispersion-shifted...

information retrieval Energy and electricity network design Grid workflow scheduling problem Inhibitory peptide design for protein protein interactions Intelligent...

when the search space is discrete (for example the traveling salesman problem, the boolean satisfiability problem, protein structure prediction, and...

deterministic methods of discrete or continuous optimization. While the force field represents only the enthalpic component of free energy (and only this component...

for predicting the 3D structures of proteins, AlphaEvolve - a coding agent for algorithm discovery that has optimized Google compute infrastructure and...

{N(N-1)}{2}}} and is, in general, greater than the energy of every Thomson problem solution. Here, N is a discrete variable that counts the number of electrons...

Evolution strategies provide a solution to parameter optimization problems for real-valued as well as discrete and mixed types of parameters. Evolutionary programming...

machines are a class of molecules typically described as an assembly of a discrete number of molecular components intended to produce mechanical movements...

performs a single mathematical operation, discrete optimization. Rainier uses quantum annealing to solve optimization problems. The D-Wave One was claimed...

bioinformatics. Let X n {\displaystyle X_{n}} and Y n {\displaystyle Y_{n}} be discrete-time stochastic processes and n ≥ 1 {\displaystyle n\geq 1} . The pair...

temperatures. Adaptation to higher temperatures is not without costs. Proteins optimized for stability at higher temperatures may show reduced flexibility...

lower activation energy. In autocatalysis a reaction product is itself a catalyst for that reaction leading to positive feedback. Proteins that act as catalysts...

changes in the thermal denaturation temperature and hence stability of a protein under varying conditions such as variations in drug concentration, buffer...

however, a nitrogen gas source may also be used. Water is known to have many discrete absorptions in the THz region that are rotational modes of water molecules...

this cyclic process. MSMs are discrete-time master equation models which describe a biomolecule's conformational and energy landscape as a set of distinct...

Engineering: discrete event and Monte-Carlo simulations (for logistics and manufacturing systems for example), queueing networks, mathematical optimization Material...