DOT2: Macromolecular docking with improved biophysical models

Combining H/D exchange mass spectroscopy and computational docking reveals extended DNA-binding surface on uracil-DNA glycosylase

(2012) Victoria A. Roberts et al.   NUCLEIC ACIDS RESEARCH

Computational Reconstruction of Multidomain Proteins Using Atomic Force Microscopy Data

(2012) Minh-Hieu Trinh et al.   STRUCTURE

ASPDock: protein-protein docking algorithm using atomic solvation parameters model

(2011) Lin Li et al.   BMC BIOINFORMATICS

On the Putative Binding Site of RFamide-Family Neuropeptides from the Western Atlantic Clam Sunray Venus and Cephalopods on Acid-Sensing Ion Channels. An Automated Docking and Molecular-Dynamics Study with hASIC1a Homology Model

(2011) Francesco Pietra   CHEMISTRY & BIODIVERSITY

XRCC4 Protein Interactions with XRCC4-like Factor (XLF) Create an Extended Grooved Scaffold for DNA Ligation and Double Strand Break Repair

(2011) Michal Hammel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Binding conformation prediction between human acetylcholinesterase and cytochrome c using molecular modeling methods

(2011) Songmi Kim et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Molecular model of hexokinase binding to the outer mitochondrial membrane porin (VDAC1): Implication for the design of new cancer therapies

(2011) Camillo Rosano   MITOCHONDRION

Packaging HIV Virion Components through Dynamic Equilibria of a Human tRNA Synthetase†

(2010) Min Guo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking

(2010) E. Mashiach et al.   NUCLEIC ACIDS RESEARCH

An integrated suite of fast docking algorithms

(2010) Efrat Mashiach et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

ReplicOpter: A replicate optimizer for flexible docking

(2010) Omar N. A. Demerdash et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Human immunodeficiency virus type 1 Vpr: oligomerization is an essential feature for its incorporation into virus particles

(2010) Narasimhan J Venkatachari et al.   Virology Journal

Targeting of the protein interaction site between FAK and IGF-1R

(2009) Donghang Zheng et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Coactosin-like protein functions as a stabilizing chaperone for 5-lipoxygenase: role of tryptophan 102

(2009) Julia Esser et al.   BIOCHEMICAL JOURNAL

FRODOCK: a new approach for fast rotational protein–protein docking

(2009) José Ignacio Garzon et al.   BIOINFORMATICS

Phylogenesis of brain-derived neurotrophic factor (BDNF)‏ in vertebrates

(2009) Gianluca Tettamanti et al.   GENE

Integrating ELF4 into the circadian system through combined structural and functional studies

(2009) Elsebeth Kolmos et al.   HFSP Journal

$F^2$Dock: Fast Fourier Protein-Protein Docking

(2009) C L Bajaj et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

SUMOylation of nuclear actin

(2009) Wilma A. Hofmann et al.   JOURNAL OF CELL BIOLOGY

Docking and MD Simulations of the Interaction of the Tarantula Peptide Psalmotoxin-1 with ASIC1a Channels Using a Homology Model

(2009) Francesco Pietra   Journal of Chemical Information and Modeling

Active-Site Gating Regulates Substrate Selectivity in a Chymotrypsin-Like Serine Protease

(2009) Troy A. Johnson et al.   JOURNAL OF MOLECULAR BIOLOGY

XPD Helicase Structures and Activities: Insights into the Cancer and Aging Phenotypes from XPD Mutations

(2008) Li Fan et al.   CELL

Structural characterization of CalO2: A putative orsellinic acid P450 oxidase in the calicheamicin biosynthetic pathway

(2008) Jason G. McCoy et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Electrostatics in protein-protein docking

(2002) Alexander Heifetz et al.   PROTEIN SCIENCE