Volarea - A Bioinformatics Tool to Calculate the Surface Area and the Volume of Molecular Systems

Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations

(2012) Junmei Wang et al.   Journal of Chemical Information and Modeling

CompASM: an Amber-VMD alanine scanning mutagenesis plug-in

(2012) João V. Ribeiro et al.   THEORETICAL CHEMISTRY ACCOUNTS

MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories

(2011) Peter Schmidtke et al.   BIOINFORMATICS

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

PocketMatch: A new algorithm to compare binding sites in protein structures

(2009) Kalidas Yeturu et al.   BMC BIOINFORMATICS

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

McVol - A program for calculating protein volumes and identifying cavities by a Monte Carlo algorithm

(2009) Mirco S. Till et al.   JOURNAL OF MOLECULAR MODELING

Molecular determinants of ligand specificity in family 11 carbohydrate binding modules - an NMR, X-ray crystallography and computational chemistry approach

(2008) Aldino Viegas et al.   FEBS Journal

Carbohydrate-binding modules from family 11: Understanding the binding mode of polysaccharides

(2008) N. F. Brás et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

MADAMM: A multistaged docking with an automated molecular modeling protocol

(2008) N. M. F. S. A. Cerqueira et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures

(2008) Bosco K Ho et al.   BMC STRUCTURAL BIOLOGY