Literature DB >> 10522241

Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems.

J Marelius1, K Kolmodin, I Feierberg, J Aqvist.   

Abstract

A new molecular dynamics program for free energy calculations in biomolecular systems is presented. It is principally designed for free energy perturbation simulations, empirical valence bond calculations, and binding affinity estimation by linear interaction energy methods. Evaluation of ligand-binding selectivity and free energy profiles for nucleophile activation in two protein tyrosine phosphatases as well as absolute binding affinity estimation for a lysine-binding protein are given as examples.

Mesh：

Substances：

Year:  1998        PMID： 10522241     DOI： 10.1016/s1093-3263(98)80006-5

Source DB:  PubMed          Journal:  J Mol Graph Model        ISSN： 1093-3263            Impact factor:   2.518


  93 in total

1.  A new binding mode of competitive antagonists to metabotropic glutamate receptors exemplified by the mGluR1-receptor antagonist AIDA (RS-aminoindan-1,5-dicarboxylic acid).

Authors:  M S Belenikin; I I Baskin; V A Palyulin; N S Zefirov
Journal:  Dokl Biochem Biophys       Date:  2002 May-Jun       Impact factor: 0.788

2.  Trypsin specificity as elucidated by LIE calculations, X-ray structures, and association constant measurements.

Authors:  Hanna-Kirsti Schrøder Leiros; Bjørn Olav Brandsdal; Ole Andreas Andersen; Vibeke Os; Ingar Leiros; Ronny Helland; Jacek Otlewski; Nils Peder Willassen; Arne O Smalås
Journal:  Protein Sci       Date:  2004-04       Impact factor: 6.725

3.  Principles of stop-codon reading on the ribosome.

Authors:  Johan Sund; Martin Andér; Johan Aqvist
Journal:  Nature       Date:  2010-05-30       Impact factor: 49.962

4.  pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA.

Authors:  Magnus Johansson; Ka-Weng Ieong; Stefan Trobro; Peter Strazewski; Johan Åqvist; Michael Y Pavlov; Måns Ehrenberg
Journal:  Proc Natl Acad Sci U S A       Date:  2010-12-17       Impact factor: 11.205

5.  Enzyme catalysis by entropy without Circe effect.

Authors:  Masoud Kazemi; Fahmi Himo; Johan Åqvist
Journal:  Proc Natl Acad Sci U S A       Date:  2016-01-11       Impact factor: 11.205

6.  Molecular dynamics simulation and linear interaction energy study of D-Glu-based inhibitors of the MurD ligase.

Authors:  Andrej Perdih; Gerhard Wolber; Tom Solmajer
Journal:  J Comput Aided Mol Des       Date:  2013-08-30       Impact factor: 3.686

7.  Mechanism of peptide bond synthesis on the ribosome.

Authors:  Stefan Trobro; Johan Aqvist
Journal:  Proc Natl Acad Sci U S A       Date:  2005-08-22       Impact factor: 11.205

8.  Probing the effect of point mutations at protein-protein interfaces with free energy calculations.

Authors:  Martin Almlöf; Johan Aqvist; Arne O Smalås; Bjørn O Brandsdal
Journal:  Biophys J       Date:  2005-11-04       Impact factor: 4.033

9.  Computer simulations of protein functions: searching for the molecular origin of the replication fidelity of DNA polymerases.

Authors:  Jan Florián; Myron F Goodman; Arieh Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  2005-04-29       Impact factor: 11.205

10.  Ligand binding to the voltage-gated Kv1.5 potassium channel in the open state--docking and computer simulations of a homology model.

Authors:  Martin Andér; Victor B Luzhkov; Johan Aqvist
Journal:  Biophys J       Date:  2007-09-28       Impact factor: 4.033
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.