scholarly journals Front Cover: Impressive Enrichment of Semiempirical Quantum Mechanics‐Based Scoring Function: HSP90 Protein with 4541 Inhibitors and Decoys (ChemPhysChem 21/2019)

ChemPhysChem ◽  
2019 ◽  
Vol 20 (21) ◽  
pp. 2718-2718
Author(s):  
Saltuk M. Eyrilmez ◽  
Cemal Köprülüoğlu ◽  
Jan Řezáč ◽  
Pavel Hobza
Keyword(s):  
Quantum Mechanics ◽  
Scoring Function ◽  
Front Cover ◽  
Hsp90 Protein

Impressive Enrichment of Semiempirical Quantum Mechanics‐Based Scoring Function: HSP90 Protein with 4541 Inhibitors and Decoys

ChemPhysChem ◽  
2019 ◽  
Vol 20 (21) ◽  
pp. 2759-2766 ◽  
Author(s):  
Saltuk M. Eyrilmez ◽  
Cemal Köprülüoğlu ◽  
Jan Řezáč ◽  
Pavel Hobza
Keyword(s):  
Quantum Mechanics ◽  
Scoring Function ◽  
Hsp90 Protein

scholarly journals Impressive Enrichment of Semiempirical Quantum Mechanics‐Based Scoring Function: HSP90 Protein with 4541 Inhibitors and Decoys

ChemPhysChem ◽  
2019 ◽  
Vol 20 (21) ◽  
pp. 2721-2721
Author(s):  
Saltuk M. Eyrilmez ◽  
Cemal Köprülüoğlu ◽  
Jan Řezáč ◽  
Pavel Hobza
Keyword(s):  
Quantum Mechanics ◽  
Scoring Function ◽  
Hsp90 Protein

A quantum mechanics-based halogen bonding scoring function for protein-ligand interactions

2015 ◽  
Vol 21 (6) ◽  
Author(s):  
Zhuo Yang ◽  
Yingtao Liu ◽  
Zhaoqiang Chen ◽  
Zhijian Xu ◽  
Jiye Shi ◽  
...  
Keyword(s):  
Quantum Mechanics ◽  
Scoring Function ◽  
Halogen Bonding ◽  
Protein Ligand Interactions ◽  
Ligand Interactions

scholarly journals Front Cover: SQM/COSMO Scoring Function: Reliable Quantum‐Mechanical Tool for Sampling and Ranking in Structure‐Based Drug Design (ChemPlusChem 11/2020)

ChemPlusChem ◽  
2020 ◽  
Vol 85 (11) ◽  
pp. 2357-2357
Author(s):  
Adam Pecina ◽  
Saltuk M. Eyrilmez ◽  
Cemal Köprülüoğlu ◽  
Vijay Madhav Miriyala ◽  
Martin Lepšík ◽  
...  
Keyword(s):  
Drug Design ◽  
Scoring Function ◽  
Quantum Mechanical ◽  
Structure Based Drug Design ◽  
Front Cover ◽  
Mechanical Tool

Docking Methodologies and Recent Advances

Oncology ◽  
2017 ◽  
pp. 804-828 ◽  
Author(s):  
Ashwani Kumar ◽  
Ruchika Goyal ◽  
Sandeep Jain
Keyword(s):  
Quantum Mechanics ◽  
Scoring Function ◽  
Scoring Functions ◽  
Post Processing ◽  
Hybrid Techniques ◽  
Knowledge Based ◽  
Recent Advances ◽  
Modern Drug ◽  
Consensus Scoring ◽  
Covalent Docking

Docking, a molecular modelling method, has wide applications in identification and optimization in modern drug discovery. This chapter addresses the recent advances in the docking methodologies like fragment docking, covalent docking, inverse docking, post processing, hybrid techniques, homology modeling etc. and its protocol like searching and scoring functions. Advances in scoring functions for e.g. consensus scoring, quantum mechanics methods, clustering and entropy based methods, fingerprinting, etc. are used to overcome the limitations of the commonly used force-field, empirical and knowledge based scoring functions. It will cover crucial necessities and different algorithms of docking and scoring. Further different aspects like protein flexibility, ligand sampling and flexibility, and the performance of scoring function will be discussed.

Docking Methodologies and Recent Advances

2016 ◽  
pp. 295-319
Author(s):  
Ashwani Kumar ◽  
Ruchika Goyal ◽  
Sandeep Jain
Keyword(s):  
Quantum Mechanics ◽  
Scoring Function ◽  
Scoring Functions ◽  
Post Processing ◽  
Hybrid Techniques ◽  
Knowledge Based ◽  
Recent Advances ◽  
Modern Drug ◽  
Consensus Scoring ◽  
Covalent Docking

Docking, a molecular modelling method, has wide applications in identification and optimization in modern drug discovery. This chapter addresses the recent advances in the docking methodologies like fragment docking, covalent docking, inverse docking, post processing, hybrid techniques, homology modeling etc. and its protocol like searching and scoring functions. Advances in scoring functions for e.g. consensus scoring, quantum mechanics methods, clustering and entropy based methods, fingerprinting, etc. are used to overcome the limitations of the commonly used force-field, empirical and knowledge based scoring functions. It will cover crucial necessities and different algorithms of docking and scoring. Further different aspects like protein flexibility, ligand sampling and flexibility, and the performance of scoring function will be discussed.

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