The book summarizes modern approaches to computer modeling of the spatial structure of proteins, including methods of conformational NMR analysis, ab initio folding, comparative modeling, simulation of thermal annealing, molecular dynamics, molecular docking and a number of others. Various aspects of the problem of molecular modeling of protein structure are considered. A critical analysis of the methods is given, the corresponding algorithms are described and examples of their application for predicting protein structures are given. Particular attention is paid to the practical use of in silico protein structure modeling methods for the design of potential drug products.