Proia, Eleonora Ragno, Alessio Antonini, Lorenzo Sabatino, Manuela Mladenovič, Milan Capobianco, Roberto Ragno, Rino
Published in
Journal of Computer-Aided Molecular Design
The main protease (Mpro) of SARS-Cov-2 is the essential enzyme for maturation of functional proteins implicated in viral replication and transcription. The peculiarity of its specific cleavage site joint with its high degree of conservation among all coronaviruses promote it as an attractive target to develop broad-spectrum inhibitors, with high se...
Hudson, Phillip S. Aviat, Félix Meana-Pañeda, Rubén Warrensford, Luke Pollard, Benjamin C. Prasad, Samarjeet Jones, Michael R. Woodcock, H. Lee Brooks, Bernard R.
Published in
Journal of Computer-Aided Molecular Design
Accurately predicting free energy differences is essential in realizing the full potential of rational drug design. Unfortunately, high levels of accuracy often require computationally expensive QM/MM Hamiltonians. Fortuitously, the cost of employing QM/MM approaches in rigorous free energy simulation can be reduced through the use of the so-called...
Medina-Franco, José L Sánchez-Cruz, Norberto López-López, Edgar Díaz-Eufracio, Bárbara I
Published in
Journal of computer-aided molecular design
The concept of chemical space is a cornerstone in chemoinformatics, and it has broad conceptual and practical applicability in many areas of chemistry, including drug design and discovery. One of the most considerable impacts is in the study of structure-property relationships where the property can be a biological activity or any other characteris...
Grosjean, Harold Işık, Mehtap Aimon, Anthony Mobley, David Chodera, John von Delft, Frank Biggin, Philip C
Published in
Journal of computer-aided molecular design
A novel crystallographic fragment screening data set was generated and used in the SAMPL7 challenge for protein-ligands. The SAMPL challenges prospectively assess the predictive power of methods involved in computer-aided drug design. Application of various methods to fragment molecules are now widely used in the search for new drugs. However, ther...
Dutta, Nivedita Deb, Indrajit Sarzynska, Joanna Lahiri, Ansuman
Published in
Journal of computer-aided molecular design
Pseudouridine is one of the most abundant post-transcriptional modifications in RNA. We have previously shown that the FF99-derived parameters for pseudouridine and some of its naturally occurring derivatives in the AMBER distribution either alone or in combination with the revised γ torsion parameters (parmbsc0) failed to reproduce their conformat...
Ries, Benjamin Rieder, Salomé Rhiner, Clemens Hünenberger, Philippe H Riniker, Sereina
Published in
Journal of computer-aided molecular design
The calculation of relative binding free energies (RBFE) involves the choice of the end-state/system representation, of a sampling approach, and of a free-energy estimator. System representations are usually termed "single topology" or "dual topology". As the terminology is often used ambiguously in the literature, a systematic categorization of th...
Sun, Qinfang Biswas, Avik Vijayan, R. S. K. Craveur, Pierrick Forli, Stefano Olson, Arthur J. Castaner, Andres Emanuelli Kirby, Karen A. Sarafianos, Stefan G. Deng, Nanjie
...
Published in
Journal of Computer-Aided Molecular Design
We have identified novel HIV-1 capsid inhibitors targeting the PF74 binding site. Acting as the building block of the HIV-1 capsid core, the HIV-1 capsid protein plays an important role in the viral life cycle and is an attractive target for antiviral development. A structure-based virtual screening workflow for hit identification was employed, whi...
Gan, Jessie Low Kumar, Dhruv Chen, Cynthia Taylor, Bryn C. Jagger, Benjamin R. Amaro, Rommie E. Lee, Christopher T.
Published in
Journal of Computer-Aided Molecular Design
The discovery of new drugs is a time consuming and expensive process. Methods such as virtual screening, which can filter out ineffective compounds from drug libraries prior to expensive experimental study, have become popular research topics. As the computational drug discovery community has grown, in order to benchmark the various advances in met...
Ries, Benjamin Normak, Karl Weiß, R Gregor Rieder, Salomé Barros, Emília P Champion, Candide König, Gerhard Riniker, Sereina
Published in
Journal of computer-aided molecular design
The calculation of relative free-energy differences between different compounds plays an important role in drug design to identify potent binders for a given protein target. Most rigorous methods based on molecular dynamics simulations estimate the free-energy difference between pairs of ligands. Thus, the comparison of multiple ligands requires th...
Waibl, Franz Kraml, Johannes Fernández-Quintero, Monica L Loeffler, Johannes R Liedl, Klaus R
Published in
Journal of computer-aided molecular design
Hydration thermodynamics play a fundamental role in fields ranging from the pharmaceutical industry to environmental research. Numerous methods exist to predict solvation thermodynamics of compounds ranging from small molecules to large biomolecules. Arguably the most precise methods are those based on molecular dynamics (MD) simulations in explici...
