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Updated: Jan 13, 2026

Molecular Spring Constant Analysis by Biomembrane Force Probe Spectroscopy
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结合流 (BindFlow):一个免费的,用户友好的管道,用于使用自由能量扰动或MM(PB/GB) SA的绝对有约束力的自由能量计算

Alejandro Martínez León1, Lucas Andersen1, Jochen S Hub1

  • 1Theoretical Physics and Center for Biophysics, Universität des Saarlandes, 66123 Saarbrücken, Germany.

Journal of chemical theory and computation
|January 7, 2026
PubMed
概括

BindFlow是一个新的,开源的Python软件,用于自动化绝对绑定自由能量 (ABFE) 计算. 它提供了一个用户友好的工具来预测与现有方法相比的受体-连接体亲和力.

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Calculating Standard Free Energy Changes02:49

Calculating Standard Free Energy Changes

The free energy change for a reaction that occurs under the standard conditions of 1 bar pressure and at 298 K is called the standard free energy change. Since free energy is a state function, its value depends only on the conditions of the initial and final states of the system. A convenient and common approach to the calculation of free energy changes for physical and chemical reactions is by use of widely available compilations of standard state thermodynamic data. One method involves the...
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The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
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Gibbs Free Energy

One of the challenges of using the second law of thermodynamics to determine if a process is spontaneous is that it requires measurements of the entropy change for the system and the entropy change for the surroundings. An alternative approach involving a new thermodynamic property defined in terms of system properties only was introduced in the late nineteenth century by American mathematician Josiah Willard Gibbs. This new property is called the Gibbs free energy (G) (or simply the free...
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Bond Dissociation Energy and Activation Energy

Bond energy is the energy required to break a bond homolytically. These values are usually expressed in units of kcal/mol or kJ/mol and are referred to as bond dissociation energies when given for specific bonds or average bond energies when indicated for a given type of bond over many compounds. Firstly, the bond dissociation energy for a single bond is weaker than that of a double bond, which in turn is weaker than that of a triple bond. Secondly, hydrogen forms relatively strong bonds with...
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Gibbs Free Energy and Thermodynamic Favorability

The spontaneity of a process depends upon the temperature of the system. Phase transitions, for example, will proceed spontaneously in one direction or the other depending upon the temperature of the substance in question. Likewise, some chemical reactions can also exhibit temperature-dependent spontaneities. To illustrate this concept, the equation relating free energy change to the enthalpy and entropy changes for the process is considered:
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