Knowledge-based energy functions for computational studies of proteins

This chapter discusses theoretical framework and methods for developing knowledge-based potential functions essential for protein structure prediction, protein-protein interaction, and protein sequence design. We discuss in some details about the Miyazawa-Jernigan contact statistical potential, distance-dependent statistical potentials, as well as geometric statistical potentials. We also describe a geometric model for developing both linear and non-linear potential functions by optimization. Applications of knowledge-based potential functions in protein-decoy discrimination, in protein-protein interactions, and in protein design are then described. Several issues of knowledge-based potential functions are finally discussed.Comment: 57 pages, 6 figures. To be published in a book by Springe

The Final Stage of Mongol Invasion of Europe: A Military Force and Secret Diplomacy (1) »

The paper analyzes the sources of information on the direct contact of the Emperor Frederick II with the Mongols before the attack of the latter on Europe, the persistent rumors of his collusion with the invaders, who came to blow mainly to the enemies of Frederick, the refusal of the Emperor of an armed clash with the Tatars, the refusal to participate in the Crusade prepared by the German prelates against the Tatars, but instead – a withdrawal of the imperial troops in Italy and the siege of Rome in order to force the pope to recognize the supremacy of the Emperor, the sudden retreat of the Tartars themselves from the German border and the abandonment of the original plans for the conquest of Germany, unexpected counteraction against Frederick of the German prelates who had been previously loyal to the Emperor and who accused him of a serious crime against the Church and the whole of Christianity. The author concludes that the Emperor Frederick and the leaders of the Western Mongol campaign were associated with secret mutual obligations. Many of his contemporaries were aware of the Emperor’s secret contacts with the Tartars (Albert von Beheim, Matthew Paris, and others.). The author analyzes the information and is trying to separate the elements of political propaganda from the established facts. The Emperor’s conspiracy with the Tatar leaders is indicated both by direct evidence and numerous indirect information analyzed in the article. On the one hand, the Emperor did everything possible to avoid a direct military confrontation with the Tatars and disrupt plans of his supporters in Germany to combat the invaders. On the other hand, the Tatar impact in Europe fell entirely on the Friedrich’s enemies who took the side of the pope in the latter’s conflict with Emperor. As a result of the Tatar invasion of Europe position of the Emperor in his confrontation with the Roman church greatly strengthened. This change in the balance of power obviously angered the church prelates and the subsequent rebellion of the German Bishops against Friedrich provoked long civil war in Germany

“…We do not know, who are they, where are they from and what are their aims”. The Mongol Expansion in the Light of Published Latin Sources

This article is primarily dedicated to the monograph of R. Hautala “From ‘David, King of the Indies’ to ‘Detestable Plebs of Satan’: An Anthology of Early Latin Information about the Tatar-Mongols”. One can find that this anthology is the most complete collection of Latin sources, which were created before the Mongol invasion of the European states and concerning the Mongols, their genesis and aims of the Western campaign. The authors state that the mentioned study includes not only the high-level presentation of handwritten artifacts, but extensive research, providing a number of original and decisive conclusions as well. On the other hand, the authors of the paper mention complexes of sources, which could provide more detailed image of diplomatic relations between European monarchs and heads of the Mongol armies, Christian interpretations of threating and unknown enemy who unexpectedly appeared on the boarders of Catholic world. Particularly, the authors point on the fragment from Alberic of Trois-Fontaines, which could be described not only as a source on the Russian-Mongol battle, as well as on the sources on diplomatic relations between the Holy Roman Empire and Mongol rulers, Russian sources that had own impact on the European scholars’ eschatological interpretations of the Tatar invasion