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Majeux, Nicolas; Scarsi, Marco; Tenette-Souaille, Catherine; Caflisch, Amedeo

doi:10.1023/a:1008785123705

Cited by 8 publications

(9 citation statements)

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“…The process of preparing electrostatic potential surfaces in this way, especially with protein/active-substance complexes, is known as comparative molecular field analysis (CoMFA); [150] . [152] Combinatorial syntheses that take advantage of dynamic libraries [153] (for an example see Scheme S6 in the Supporting Information) increase the amount of experimentally accessible data by orders of magnitude; this technique is also being used more and more for the exploration of intermolecular forces. [152] Combinatorial syntheses that take advantage of dynamic libraries [153] (for an example see Scheme S6 in the Supporting Information) increase the amount of experimentally accessible data by orders of magnitude; this technique is also being used more and more for the exploration of intermolecular forces.…”

Section: Lfer and Qspr/qsar Experiments Analyses With Protein Complexesmentioning

confidence: 99%

“…With programs such as GRID, [151] surfaces are "felt" in computer simulations by, for example, hydrophobic or hydrophilic test molecules. [152] Combinatorial syntheses that take advantage of dynamic libraries [153] (for an example see Scheme S6 in the Supporting Information) increase the amount of experimentally accessible data by orders of magnitude; this technique is also being used more and more for the exploration of intermolecular forces. [154] A comprehensive analysis of a great many complexes with biopolymers gave, for the "best" ligands, a rough correlation with the increasing number of non-hydrogen atoms, thereby leading to an affinity of about 6 kJ mol À1 per heavy atom with ligands that were not too large.…”

Section: Lfer and Qspr/qsar Experiments Analyses With Protein Complexesmentioning

confidence: 99%

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Binding Mechanisms in Supramolecular Complexes

2009

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Supramolecular chemistry has expanded dramatically in recent years both in terms of potential applications and in its relevance to analogous biological systems. The formation and function of supramolecular complexes occur through a multiplicity of often difficult to differentiate noncovalent forces. The aim of this Review is to describe the crucial interaction mechanisms in context, and thus classify the entire subject. In most cases, organic host-guest complexes have been selected as examples, but biologically relevant problems are also considered. An understanding and quantification of intermolecular interactions is of importance both for the rational planning of new supramolecular systems, including intelligent materials, as well as for developing new biologically active agents.

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Section: Lfer and Qspr/qsar Experiments Analyses With Protein Complexesmentioning

confidence: 99%

Section: Lfer and Qspr/qsar Experiments Analyses With Protein Complexesmentioning

confidence: 99%

Binding Mechanisms in Supramolecular Complexes

2009

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“…B. mit hydrophoben oder hydrophilen Testmolekülen "abgetastet". [152] Kombinatorische Synthesen unter Einschluss dynamischer Bibliotheken [153] (Beispiel Schema S6) ermöglichen die Potenzierung des experimentell zugänglichen Datenmaterials, was zunehmend auch für die Explorierung zwischenmolekularer Kräfte genutzt wird. [154] Eine zusammenfassende Analyse zahlreicher Komplexe mit Biopolymeren ergab für die "besten" Liganden eine ungefähre Korrelation mit der zunehmenden Zahl von NichtWasserstoffatomen, mit einer Affinität von etwa 6 kJ mol…”

Section: Quantifizierung Von Bindungsbeiträgen In Lösungunclassified

Bindungsmechanismen in supramolekularen Komplexen

Schneider

2009

Angewandte Chemie

185

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Kräfte‐Sammelsurium: Supramolekulare Komplexe, wie der gezeigte, beruhen meist auf einer Kombination unterschiedlichster Wechselwirkungen, wie Ionenpaarbildung, Wasserstoffbrücken und Stapelwechselwirkungen. Die nicht immer einfache Charakterisierung von Natur und Stärke der intermolekularen Kräfte liefert Beiträge zum Verständnis biomimetischer Systeme wie auch zum Design von synthetischen Rezeptoren, Wirkstoffen und intelligenten Materialien. Die supramolekulare Chemie hat in den letzten Jahren eine enorme Ausdehnung erfahren, sowohl mit Blick auf mögliche Anwendungen wie auch auf analoge biologische Systeme. Bildung und Funktion supramolekularer Komplexe werden durch eine Vielzahl von oft schwer zu differenzierenden nichtkovalenten Kräften bestimmt. Ziel dieses Aufsatzes ist es, die entscheidenden Wechselwirkungsmechanismen zusammenhängend darzustellen und das Gesamtgebiet auf diese Weise zu klassifizieren. Als Beispiele werden meist organische Wirt‐Gast‐Komplexe gewählt, unter Berücksichtigung auch von biologisch relevanten Fragestellungen. Das Verständnis und die Quantifizierung der intermolekularen Wechselwirkungen ist für die rationale Planung neuer supramolekularer Systeme, einschließlich intelligenter Materialien, ebenso von Bedeutung wie für die Entwicklung neuer Wirkstoffe.

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“…The first type is well known; it comes from the many‐body character of the solvation energy, mentioned above. This effect has already been studied, and approximate pairwise decomposition methods have been proposed for both SA and GB terms, and also for PB terms . Here, to make the solvation energy pairwise additive, we use a GB “Native Environment” approximation (NEA), presented earlier, and an improved pairwise decomposition for the SA terms, presented here.…”

Section: Introductionmentioning

confidence: 99%

Pairwise decomposition of an MMGBSA energy function for computational protein design

Gaillard

Simonson

2014

J Comput Chem

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Computational protein design (CPD) aims at predicting new proteins or modifying existing ones. The computational challenge is huge as it requires exploring an enormous sequence and conformation space. The difficulty can be reduced by considering a fixed backbone and a discrete set of sidechain conformations. Another common strategy consists in precalculating a pairwise energy matrix, from which the energy of any sequence/conformation can be quickly obtained. In this work, we examine the pairwise decomposition of protein MMGBSA energy functions from a general theoretical perspective, and an implementation proposed earlier for CPD. It includes a Generalized Born term, whose many-body character is overcome using an effective dielectric environment, and a Surface Area term, for which we present an improved pairwise decomposition. A detailed evaluation of the error introduced by the decomposition on the different energy components is performed. We show that the error remains reasonable, compared to other uncertainties.

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Cited by 8 publications

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Binding Mechanisms in Supramolecular Complexes

Binding Mechanisms in Supramolecular Complexes

Bindungsmechanismen in supramolekularen Komplexen

Pairwise decomposition of an MMGBSA energy function for computational protein design

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