CDOCKER and $$\lambda$$-dynamics for prospective prediction in D3R Grand Challenge 2

نویسندگان
چکیده

برای دانلود باید عضویت طلایی داشته باشید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2

We present the performance of HADDOCK, our information-driven docking software, in the second edition of the D3R Grand Challenge. In this blind experiment, participants were requested to predict the structures and binding affinities of complexes between the Farnesoid X nuclear receptor and 102 different ligands. The models obtained in Stage1 with HADDOCK and ligand-specific protocol show an ave...

متن کامل

Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking

We have studied the binding of 102 ligands to the farnesoid X receptor within the D3R Grand Challenge 2016 blind-prediction competition. First, we employed docking with five different docking software and scoring functions. The selected docked poses gave an average root-mean-squared deviation of 4.2 Å. Consensus scoring gave decent results with a Kendall's τ of 0.26 ± 0.06 and a Spearman's ρ of...

متن کامل

The Burnett Problem: Molecular Dynamics' Grand Challenge

The nonlinear Burnett coeecients are the Tay-lor series coeecients for the functional dependence describing how the Thermodynamic Flux responds to a Thermodynamic Force acting on a uid. Ernst et. al. computed the functional dependence exactly for a hard disk/sphere uid (a uid made up of idealised billiard balls) undergoing shear ow, and found that the relationship was non-analytic, i.e. that th...

متن کامل

simulation and experimental studies for prediction mineral scale formation in oil field during mixing of injection and formation water

abstract: mineral scaling in oil and gas production equipment is one of the most important problem that occurs while water injection and it has been recognized to be a major operational problem. the incompatibility between injected and formation waters may result in inorganic scale precipitation in the equipment and reservoir and then reduction of oil production rate and water injection rate. ...

Blinded predictions of binding modes and energies of HSP90-α ligands for the 2015 D3R grand challenge.

In the framework of the 2015 D3R inaugural grand challenge, blind binding pose and affinity predictions were performed for a set of 180 ligands of the Heat Shock Protein HSP90-α protein, a relevant cancer target. Spectral clustering was used to rapidly identify alternative binding site conformations in publicly available crystallographic HSP90-α structures. Subsequently, multiple docking and sc...

متن کامل

ذخیره 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 Computer-Aided Molecular Design

سال: 2017

ISSN: 0920-654X,1573-4951

DOI: 10.1007/s10822-017-0050-5