BAR(Bennett Acceptance Ratio) 알고리즘을 기반으로 한 free energy 계산 모듈입니다. 결합 상태와 비결합 상태 사이의 변화를 여러 중간 상태(λ)로 나누어 각각 샘플링한 후, 상태간 free energy 차이를 계산하여 최종 자유에너지를 산출합니다. CANDDIE에서는 λ 구성, 샘플링 및 계산 workflow를 자체적으로 구현, 최적화하여 제공합니다.
세 모듈 중 계산 과정이 가장 정교한 대신 계산량이 크고 충분한 sampling이 필요합니다. 따라서 초기 대규모 스크리닝보다는 선별된 소수 화합물의 정밀한 상대 순위 평가에 적합합니다.
MM-GBSA (Molecular Mechanics-Generalized Born Surface Area)
BARon처럼 여러 λ 중간 상태를 거치지 않고, MD trajectory에서 얻은 구조를 이용하여 분자역학적 상호작용 에너지와 용매화 에너지 등을 결합해 binding free energy를 추정하는 방법입니다. 정전기적 용매화 효과는 Generalized Born(GB) 모델로 근사하기 때문에 비교적 빠르게 계산할 수 있습니다. CANDDIE에서는 Atomatrix가 자체 구현·최적화한 알고리즘으로 제공합니다.
기본적인 계산 개념은 MM-GBSA와 유사한 방식이지만, 정전기 용매화 에너지를 GB 근사 대신 Poisson-Boltzmann(PB) 방정식을 수치적으로 풀어 계산합니다. 따라서 electrostatic solvation을 보다 상세하게 다루는 대신 MM-GBSA보다 계산 비용이 증가합니다. CANDDIE에서는 이 역시 자체 구현, 최적화하여 제공합니다.
정전기적 상호작용의 영향을 보다 상세하게 평가할 필요가 있는 시스템에서 활용할 수 있으며, 특히 전하를 띤 ligand나 binding site를 분석할 때 함께 검토하기에 유용합니다.
BARon, MM-GBSA, MM-PBSA는 계산 원리와 근사 수준이 서로 다르므로 산출되는 값의 절대적인 크기를 모듈 간 직접 비교해서는 안 됩니다. 화합물의 상대적 결합 경향을 비교할 때에는 동일한 모듈과 동일한 계산 조건에서 얻은 결과끼리 비교하는 것을 권장합니다.
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