Converging a Knowledge-Based Scoring Function: DrugScore2018
نویسندگان
چکیده
منابع مشابه
DrugScorePPI for scoring protein-protein interactions: improving a knowledge-based scoring function by atomtype-based QSAR
Protein-protein complexes are known to play key roles in many cellular processes. Therefore, knowledge of the three-dimensional structure of protein-complexes is of fundamental importance. A key goal in protein-protein docking is to identify near-native protein-complex structures. In this work, we address this problem by deriving a knowledge-based scoring function from protein-protein complex s...
متن کاملKnowledge-based scoring function to predict protein-ligand interactions.
The development and validation of a new knowledge-based scoring function (DrugScore) to describe the binding geometry of ligands in proteins is presented. It discriminates efficiently between well-docked ligand binding modes (root-mean-square deviation <2.0 A with respect to a crystallographically determined reference complex) and those largely deviating from the native structure, e.g. generate...
متن کاملScoring and Lessons Learned with the CSAR Benchmark Using an Improved Iterative Knowledge-Based Scoring Function
Based on a statistical mechanics-based iterative method, we have extracted a set of distance-dependent, all-atom pairwise potentials for protein-ligand interactions from the crystal structures of 1300 protein-ligand complexes. The iterative method circumvents the long-standing reference state problem in knowledge-based scoring functions. The resulted scoring function, referred to as ITScore 2.0...
متن کاملA knowledge-based scoring function based on residue triplets for protein structure prediction
One of the general paradigms for ab initio protein structure prediction involves sampling the conformational space such that a large set of decoy (candidate) structures are generated and then selecting native-like conformations from those decoys using various scoring functions. In this study, based on a physical/geometric approach first suggested by Banavar and colleagues, we formulate a knowle...
متن کاملAn iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function
We have developed an iterative knowledge-based scoring function (ITScore) to describe protein-ligand interactions. Here, we assess ITScore through extensive tests on native structure identification, binding affinity prediction, and virtual database screening. Specifically, ITScore was first applied to a test set of 100 protein-ligand complexes constructed by Wang et al. (J Med Chem 2003, 46, 22...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Journal of Chemical Information and Modeling
سال: 2018
ISSN: 1549-9596,1549-960X
DOI: 10.1021/acs.jcim.8b00582