Publication

Design of lattice proteins with explicit solvent

2002
Journal Articles

Abstract

Protein design is important to develop new drugs. As such, a knowledge of the correct model to use to design novel proteins is of the utmost importance. Here we show that a simple model where the solvent degrees of freedom are (semi)explicitly taken into account performs better than other existing models when compared to real data. Some consequences on the criteria to be used for protein design are discussed.

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2002
Journal Articles

Abstract

Official source

Related concepts (32)

Implicit solvation

Implicit solvation (sometimes termed continuum solvation) is a method to represent solvent as a continuous medium instead of individual “explicit” solvent molecules, most often used in molecular dynamics simulations and in other applications of molecular mechanics. The method is often applied to estimate free energy of solute-solvent interactions in structural and chemical processes, such as folding or conformational transitions of proteins, DNA, RNA, and polysaccharides, association of biological macromolecules with ligands, or transport of drugs across biological membranes.

Protein folding

Protein folding is the physical process where a protein chain is translated into its native three-dimensional structure, typically a "folded" conformation, by which the protein becomes biologically functional. Via an expeditious and reproducible process, a polypeptide folds into its characteristic three-dimensional structure from a random coil. Each protein exists first as an unfolded polypeptide or random coil after being translated from a sequence of mRNA into a linear chain of amino acids.

Knowledge

Knowledge is a form of awareness or familiarity. It is often understood as awareness of facts or as practical skills, and may also mean familiarity with objects or situations. Knowledge of facts, also called propositional knowledge, is often defined as true belief that is distinct from opinion or guesswork by virtue of justification. While there is wide agreement among philosophers that propositional knowledge is a form of true belief, many controversies in philosophy focus on justification.

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