Improvements in docking scoring functions: the physics-based perspective

نویسنده

  • Xavier Barril
چکیده

Docking is possibly the most widely used technique in structure-based drug design. It is recognized as extremely useful to guide the development of active molecules as well as in virtual screening to identify new leads. But docking is also notoriously imperfect and many aspects need to improve. In this talk I will present our work on two different sources of errors in the docking predictions: protein-ligand interaction potentials and internal energy of the ligands. The use of higher-level calculations offers an opportunity to obtain better quality results and offers a glimpse of the full potential of the technique, but introducing this information back into fast and general scoring functions remains a challenge.

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

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions.

The scoring function is one of the most important components in structure-based drug design. Despite considerable success, accurate and rapid prediction of protein-ligand interactions is still a challenge in molecular docking. In this perspective, we have reviewed three basic types of scoring functions (force-field, empirical, and knowledge-based) and the consensus scoring technique that are us...

متن کامل

Scoring protein-protein docked structures based on the balance and tightness of binding

One main issue in protein-protein docking is to filter or score the putative docked structures. Unlike many popular scoring functions that are based on geometric and energetic complementarity, we present a set of scoring functions that are based on the consideration of local balance and tightness of binding of the docked structures. These scoring functions include the force and moment acting on...

متن کامل

Development of A Head Docking Device for Linac-based Stereotactic Radiosurgery System to be Installed on Neptun 10 PC Linac

Introduction:  Stereotactic  radiosurgery  is  a  technique  for  the  treatment  of  intracranial  lesions  with  highly  collimated  x-ray  beam.  Linac-based  radiosurgery  is  currently  performed  by  two  techniques:  couch or pedestal mounted. In the first technique, a device is required to affix patient's head to a couch  and  moreover  to  translate  it  accurately.  Structure  of  suc...

متن کامل

Comparing Neural-Network Scoring Functions and the State of the Art: Applications to Common Library Screening

We compare established docking programs, AutoDock Vina and Schrödinger's Glide, to the recently published NNScore scoring functions. As expected, the best protocol to use in a virtual-screening project is highly dependent on the target receptor being studied. However, the mean screening performance obtained when candidate ligands are docked with Vina and rescored with NNScore 1.0 is not statist...

متن کامل

GeauxDock: A novel approach for mixed-resolution ligand docking using a descriptor-based force field

Molecular docking is an important component of computer-aided drug discovery. In this communication, we describe GeauxDock, a new docking approach that builds on the ideas of ligand homology modeling. GeauxDock features a descriptor-based scoring function integrating evolutionary constraints with physics-based energy terms, a mixed-resolution molecular representation of protein-ligand complexes...

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

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

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:

دوره 4  شماره 

صفحات  -

تاریخ انتشار 2012