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35 in total

1. Scoring functions: a view from the bench.

Authors: J R Tame
Journal: J Comput Aided Mol Des Date: 1999-03 Impact factor: 3.686

2. Evaluation of the relative stability of liganded versus ligand-free protein conformations using Simplicial Neighborhood Analysis of Protein Packing (SNAPP) method.

Authors: Douglas B Sherman; Shuxing Zhang; J Bruce Pitner; Alexander Tropsha
Journal: Proteins Date: 2004-09-01

3. Direct-coupling analysis of residue coevolution captures native contacts across many protein families.

Authors: Faruck Morcos; Andrea Pagnani; Bryan Lunt; Arianna Bertolino; Debora S Marks; Chris Sander; Riccardo Zecchina; José N Onuchic; Terence Hwa; Martin Weigt
Journal: Proc Natl Acad Sci U S A Date: 2011-11-21 Impact factor: 11.205

4. Modeling the hydration layer around proteins: HyPred.

Authors: Jouko J Virtanen; Lee Makowski; Tobin R Sosnick; Karl F Freed
Journal: Biophys J Date: 2010-09-08 Impact factor: 4.033

5. Study of intermolecular contacts in the proline-rich homeodomain (PRH)-DNA complex using molecular dynamics simulations.

Authors: Seifollah Jalili; Leila Karami
Journal: Eur Biophys J Date: 2012-02-04 Impact factor: 1.733

6. Protonation linked equilibria and apparent affinity constants: the thermodynamic profile of the alpha-chymotrypsin-proflavin interaction.

Authors: Gilles Bruylants; René Wintjens; Yvan Looze; Christina Redfield; Kristin Bartik
Journal: Eur Biophys J Date: 2007-04-19 Impact factor: 1.733

The role of water in sequence-independent ligand binding by an oligopeptide transporter protein.

1. Scoring functions: a view from the bench.

2. Evaluation of the relative stability of liganded versus ligand-free protein conformations using Simplicial Neighborhood Analysis of Protein Packing (SNAPP) method.

3. Direct-coupling analysis of residue coevolution captures native contacts across many protein families.

4. Modeling the hydration layer around proteins: HyPred.

5. Study of intermolecular contacts in the proline-rich homeodomain (PRH)-DNA complex using molecular dynamics simulations.

6. Protonation linked equilibria and apparent affinity constants: the thermodynamic profile of the alpha-chymotrypsin-proflavin interaction.

7. A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling.

8. Systematic placement of structural water molecules for improved scoring of protein-ligand interactions.

9. Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations.

Review 10. A medicinal chemist's guide to molecular interactions.