A description of Monte Carlo methods for simulation of proteins is given. Advantages and disadvantages of the Monte Carlo approach are presented. The theoretical basis for calculating equilibrium properties of biological molecules by the Monte Carlo method is presented. Some of the st ...
A method for incorporating quantum mechanics into enzyme kinetics modeling is presented. Three aspects are emphasized: 1) combined quantum mechanical and molecular mechanical methods are used to represent the potential energy surface for modeling bond forming and breaking proc ...
In the context of molecular dynamics simulations of proteins, the term “force field” refers to the combination of a mathematical formula and associated parameters that are used to describe the energy of the protein as a function of its atomic coordinates. In this review, we describe the function ...
Reliable first-principles calculations of protein—ligand binding constants can play important roles in the study and characterization of biological recognition processes and applications to drug discovery. A detailed procedure for such a calculation is outlined in this cha ...
Normal mode analysis and essential dynamics analysis are powerful methods used for the analysis of collective motions in biomolecules. Their application has led to an appreciation of the importance of protein dynamics in function and the relationship between structure and dynamic ...
Selected applications of free energy calculations to the realm of membrane proteins are reviewed. The theoretical underpinnings of these calculations are described, focusing on free energy perturbation and the use of thermodynamic integration to determine free energy changes a ...
Membrane protein structures are underrepresented in the Protein Data Bank (PDB) because of difficulties associated with expression and crystallization. As such, it is one area in which computational studies, particularly molecular dynamics (MD), can provide useful additional i ...
Implicit models of membrane environments offer computational advantages in simulations of membrane-interacting proteins and peptides. Such methods are especially useful for studies of long time scale processes, such as folding and aggregation, or very large complexes that are o ...
This chapter discusses the practical aspects of setting up molecular dynamics simulations for membrane-associated proteins and peptides. Special emphasis lies on the analysis of such systems. The main focus is the association between a cationic peptide and an anionic lipid bilayer—a ...
Three-dimensional analysis of protein structures is proving to be one of the most fruitful modes of biological and medical discovery in the early 21st century, providing fundamental insight into many (perhaps most) biochemical functions of relevance to the cause and treatment of disea ...
Elucidating the structure of transmembrane proteins domains with high-resolution methods is a difficult and sometimes impossible task. Here, we explain the method of combining a limited amount of experimental data with automated high-throughput molecular dynamics (MD) simul ...
Nuclear magnetic resonance (NMR) has become a well-established method to characterize the structures of biomolecules in solution. High-quality structures are now produced, thanks to both experimental and computational developments, allowing the use of new NMR parameters and im ...
Conformational changes are the hallmarks of protein dynamics and are often intimately related to protein functions. Molecular dynamics (MD) simulation is a powerful tool to study the time-resolved properties of protein structure in atomic details. In this chapter, we discuss the vari ...
A short review of the results of molecular modeling of prion disease is presented in this chapter. According to the “one-protein theory” proposed by Prusiner, prion proteins are misfolded naturally occurring proteins, which, on interaction with correctly folded proteins may induce mis ...
Computational protein folding can be classified into pathway and sampling approaches. Here, we use the AMBER simulation package as an example to illustrate the protocols for all-atom molecular simulations of protein folding, including system setup, simulation, and analysis. We int ...
The availability of three-dimensional (3D) models of both drug leads (small molecule ligands) and drug targets (proteins) is essential to molecular docking and computational drug discovery. This chapter describes an emerging methodology that can be used to identify both drug leads and ...
An important contribution to today's computer-aided drug design is the automated screening of large compound databases against structurally resolved protein receptors targets. The introduction of ligand flexibility has, by now, become a standardized procedure. In contrast, a g ...
Molecular docking is a key tool in structural molecular biology and computer-assisted drug design. The goal of ligand—protein docking is to predict the predominant binding mode(s) of a ligand with a protein of known three-dimensional structure. Successful docking methods search high- ...
Sequence alignment remains a fundamental task in bioinformatics. The literature contains programs that employ a host of exact and heuristic strategies available in computer science. Probcons was the first program to construct maximum expected accuracy sequence alignments with ...
This chapter outlines several methods implemented in the MAFFT package. MAFFT is a popular multiple sequence alignment (MSA) program with various options for the progressive method, the iterative refinement method and other methods. We first outline basic usage of MAFFT and then descri ...
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