Protein Structure and Dynamics

Motivation: The identification of novel drug-target (DT) interactions is a substantial part of the drug discovery process. Most of the computational methods that have been proposed to predict DT interactions have focused on binary classification, where the goal is to determine whether a DT pair interacts or not. Howev…

• ARZUCAN ÖZGÜR TÜRKMEN

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• ALİ RANA ATILGAN

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• ALİ RANA ATILGAN

SUMMARY: We developed a Python package, ProDy, for structure-based analysis of protein dynamics. ProDy allows for quantitative characterization of structural variations in heterogeneous datasets of structures experimentally resolved for a given biomolecular system, and for comparison of these variations with the theor…

Vibrational dynamics of folded proteins is studied using a Gaussian model in which the protein is viewed as a network, residues representing the junctions, and the connectivity being established by a single parameter harmonic potential. Application to seven proteins showed that the local packing density plays a major…

• TÜRKAN HALİLOĞLU

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPrinciples of Protein−Protein Interactions: What are the Preferred Ways For Proteins To Interact?Ozlem Keskin, Attila Gursoy, Buyong Ma, and Ruth NussinovView Author Information Koc University, Center for Computational Biology and Bioinformatics and College of Engineering, R…

• ZEHRA ÖZLEM KESKİN ÖZKAYA

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPrinciples of Protein−Protein Interactions: What are the Preferred Ways For Proteins To Interact?Ozlem Keskin, Attila Gursoy, Buyong Ma, and Ruth NussinovView Author Information Koc University, Center for Computational Biology and Bioinformatics and College of Engineering, R…

• ATTİLA GÜRSOY

NAMD is a molecular dynamics program designed for high performance simulations of large biomolecular systems on parallel computers. An object-oriented design imple mented using C++ facilitates the incorporation of new algorithms into the program. NAMD uses spatial decom position coupled with a multithreaded, message-d…

• ATTİLA GÜRSOY

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTNormal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane ProteinsIvet Bahar*, Timothy R. Lezon†, Ahmet Bakan†, and Indira H. ShrivastavaView Author Information Department of Computational Biology, School of Medicine, University of Pittsburgh, 3064 BS…

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• FERİDE SEVERCAN

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• ZEHRA ÖZLEM KESKİN ÖZKAYA

A single-parameter harmonic Hamiltonian based on local packing density and contact topology is proposed for studying residue fluctuations in native proteins. The internal energy obeys an equipartition law, and free energy changes result from entropy fluctuations only. Frequency--wave-number maps show communication bet…

• ALİ RANA ATILGAN