Virtual screening and in silico design of novel inhibitors of bacterial lectins

by Alán, Jan, Kulhánek, Petr, Koča, Jaroslav
Published 2012

Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA

by Rázga, Filip, Koča, Jaroslav, Mokdad, Ali, Šponer, Jiří
Published 2007

How Ionic Strength Affects the Conformational Behavior of Human and Rat Beta Amyloids – A Computational Study

by Kříž, Zdeněk, Klusák, Jiří, Krištofíková, Zdena, Koča, Jaroslav
Published 2013

QM quality atomic charges for proteins

by Geidl, Stanislav, Ionescu, Crina-Maria, Vařeková, Radka Svobodová, Koča, Jaroslav
Published 2014

Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2

by Trnka, Tomáš, Kozmon, Stanislav, Tvaroška, Igor, Koča, Jaroslav
Published 2015

CAVER: a new tool to explore routes from protein clefts, pockets and cavities

by Petřek, Martin, Otyepka, Michal, Banáš, Pavel, Košinová, Pavlína, Koča, Jaroslav, Damborský, Jiří
Published 2006

Searching for tunnels of proteins – comparison of approaches and available software tools

by Jaiswal, Deepti, Vařeková, Radka Svobodová, Ionescu, Crina-Maria, Sehnal, David, Koča, Jaroslav
Published 2012

Conformations of Flanking Bases in HIV-1 RNA DIS Kissing Complexes Studied by Molecular Dynamics

by Réblová, Kamila, Fadrná, Eva, Sarzynska, Joanna, Kulinski, Tadeusz, Kulhánek, Petr, Ennifar, Eric, Koča, Jaroslav, Šponer, Jiří
Published 2007

Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation

by Ionescu, Crina-Maria, Svobodová Vařeková, Radka, Prehn, Jochen H. M., Huber, Heinrich J., Koča, Jaroslav
Published 2012

Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations

by Stadlbauer, Petr, Krepl, Miroslav, Cheatham, Thomas E., Koča, Jaroslav, Šponer, Jiří
Published 2013

Stacking Interactions between Carbohydrate and Protein Quantified by Combination of Theoretical and Experimental Methods

by Wimmerová, Michaela, Kozmon, Stanislav, Nečasová, Ivona, Mishra, Sushil Kumar, Komárek, Jan, Koča, Jaroslav
Published 2012

Nemesis - a molecular modeling package

by Štěpán, Jakub, Kulhánek, Petr, Lenčo, Milan, Střelcová, Zora, Křenek, Aleš, Koča, Jaroslav
Published 2013

Empirical charges for chemoinformatics applications

by Bouchal, Tomáš, Vařeková, Radka Svobodová, Raček, Tomáš, Ionescu, Crina-Maria, Geidl, Stanislav, Křenek, Aleš, Koča, Jaroslav
Published 2014

Consistency of sugar structures and their annotation in the PDB

by Jaiswal, Deepti, Sehnal, David, Vařeková, Radka Svobodová, Ionescu, Crina-Maria, Koča, Jaroslav
Published 2014

Electronegativity Equalization Method: Parameterization and Validation for Large Sets of Organic, Organohalogene and Organometal Molecule

by Vařeková, Radka Svobodová, Jiroušková, Zuzana, Vaněk, Jakub, Suchomel, Šimon, Koča, Jaroslav
Published 2007

Extended molecular dynamics of a c-kit promoter quadruplex

by Islam, Barira, Stadlbauer, Petr, Krepl, Miroslav, Koca, Jaroslav, Neidle, Stephen, Haider, Shozeb, Sponer, Jiri
Published 2015

PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank

by Sehnal, David, Pravda, Lukáš, Svobodová Vařeková, Radka, Ionescu, Crina-Maria, Koča, Jaroslav
Published 2015

Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations

by Stadlbauer, Petr, Kührová, Petra, Banáš, Pavel, Koča, Jaroslav, Bussi, Giovanni, Trantírek, Lukáš, Otyepka, Michal, Šponer, Jiří
Published 2015

How the methodology of 3D structure preparation influences the quality of QSPR models?

by Geidl, Stanislav, Beránek, Roman, Vařeková, Radka Svobodová, Bouchal, Tomáš, Brumovský, Miroslav, Kudera, Michal, Skřehota, Ondřej, Koča, Jaroslav
Published 2012

SiteBinder – an improved approach for comparing multiple protein structural motifs. Case studies on biologically important motifs

by Sehnal, David, Vařeková, Radka Svobodová, Huber, Heinrich J, Geidl, Stanislav, Ionescu, Crina-Maria, Wimmerová, Michaela, Koča, Jaroslav
Published 2012