Publications

2022 Excited state non-adiabatic dynamics of large photoswitchable molecules using a chemically transferable machine learning potential Eugene I. Shakhnovich · Nature communications · Scholar only 118 2021 Accelerating high-throughput virtual screening through molecular pool-based active learning Eugene I. Shakhnovich · Chemical science · Scholar only 428 2020 Dynamic metastable long-living droplets formed by sticker-spacer proteins Eugene I. Shakhnovich · Elife · Scholar only 190 2019 Common activation mechanism of class A GPCRs Eugene I. Shakhnovich · elife · Scholar only 779 2018 Differential enzyme flexibility probed using solid-state nanopores Eugene I. Shakhnovich · ACS nano · Scholar only 116 2017 Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations Eugene I. Shakhnovich · Current opinion in structural biology · Scholar only 90 2017 Evidence of evolutionary selection for cotranslational folding Eugene I. Shakhnovich · Proceedings of the National Academy of Sciences · Scholar only 123 2016 Biophysical principles predict fitness landscapes of drug resistance Eugene I. Shakhnovich · Proceedings of the National Academy of Sciences · Scholar only 167 2016 OpenGrowth: an automated and rational algorithm for finding new protein ligands Eugene I. Shakhnovich · Journal of medicinal chemistry · Scholar only 88 2015 Protein homeostasis imposes a barrier on functional integration of horizontally transferred genes in bacteria Eugene I. Shakhnovich · PLoS genetics · Scholar only 92 2014 Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics Eugene I. Shakhnovich · Current opinion in structural biology · Scholar only 104 2013 Protein quality control acts on folding intermediates to shape the effects of mutations on organismal fitness Eugene I. Shakhnovich · Molecular cell · Scholar only 207 2012 Protein biophysics explains why highly abundant proteins evolve slowly Eugene I. Shakhnovich · Cell reports · Scholar only 124 2012 Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations Eugene I. Shakhnovich · Proceedings of the National Academy of Sciences · Scholar only 122 2012 The interface of protein structure, protein biophysics, and molecular evolution Eugene I. Shakhnovich · Protein Science · Scholar only 273 2011 A biophysical protein folding model accounts for most mutational fitness effects in viruses Eugene I. Shakhnovich · Proceedings of the National Academy of Sciences · Scholar only 240 2011 Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions Eugene I. Shakhnovich · Proceedings of the National Academy of Sciences · Scholar only 117 2010 De novo design: balancing novelty and confined chemical space Eugene I. Shakhnovich · Expert opinion on drug discovery · Scholar only 126 2010 Optimality of mutation and selection in germinal centers Eugene I. Shakhnovich · PLoS computational biology · Scholar only 95 2009 All-atom model for stabilization of α-helical structure in peptides by hydrocarbon staples Eugene I. Shakhnovich · Journal of the American Chemical Society · Scholar only 154 2009 FOG: Fragment Optimized Growth Algorithm for the de Novo Generation of Molecules Occupying Druglike Chemical Space Eugene I. Shakhnovich · Journal of chemical information and modeling · Scholar only 101 2008 Constraints imposed by non-functional protein–protein interactions on gene expression and proteome size Eugene I. Shakhnovich · Molecular systems biology · Scholar only 123 2007 All-atom ab initio folding of a diverse set of proteins Eugene I. Shakhnovich · Structure · Scholar only 113 2007 Positive and negative design in stability and thermal adaptation of natural proteins Eugene I. Shakhnovich · PLoS Computational Biology · Scholar only 167 2007 Protein and DNA sequence determinants of thermophilic adaptation Eugene I. Shakhnovich · PLoS computational biology · Scholar only 419 2007 Protein stability imposes limits on organism complexity and speed of molecular evolution Eugene I. Shakhnovich · Proceedings of the National Academy of Sciences · Scholar only 330 2007 Robust protein–protein interactions in crowded cellular environments Eugene I. Shakhnovich · Proceedings of the National Academy of Sciences · Scholar only 92 2007 Structural similarity enhances interaction propensity of proteins Eugene I. Shakhnovich · Journal of molecular biology · Scholar only 143 2007 The folding mechanics of a knotted protein Eugene I. Shakhnovich · Journal of molecular biology · Scholar only 173 2006 A simple physical model for scaling in protein-protein interaction networks Eugene I. Shakhnovich · Proceedings of the National Academy of Sciences · Scholar only 137 2006 On the origin and highly likely completeness of single-domain protein structures Eugene I. Shakhnovich · Proceedings of the National Academy of Sciences · Scholar only 204 2006 Protein folding thermodynamics and dynamics: where physics, chemistry and biology meet Eugene I. Shakhnovich · Chemical reviews · Scholar only 487 2005 Entropic stabilization of proteins and its proteomic consequences Eugene I. Shakhnovich · PLoS computational biology · Scholar only 126 2005 Physics and evolution of thermophilic adaptation Eugene I. Shakhnovich · Proceedings of the National Academy of Sciences · Scholar only 364 2005 Protein structure and evolutionary history determine sequence space topology Eugene I. Shakhnovich · Genome research · Scholar only 109 2005 Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations Eugene I. Shakhnovich · Journal of molecular biology · Scholar only 97 2004 Commitment and nucleation in the protein G transition state Eugene I. Shakhnovich · Journal of molecular biology · Scholar only 92 2003 Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases Eugene I. Shakhnovich · Proceedings of the National Academy of Sciences · Scholar only 114 2003 Natural selection of more designable folds: a mechanism for thermophilic adaptation Eugene I. Shakhnovich · Proceedings of the National Academy of Sciences · Scholar only 119 2003 Structural determinant of protein designability Eugene I. Shakhnovich · Physical review letters · Scholar only 153 2002 A structure-based method for derivation of all-atom potentials for protein folding Eugene I. Shakhnovich · Proceedings of the National Academy of Sciences · Scholar only 91 2002 Combinatorial computational method gives new picomolar ligands for a known enzyme Eugene I. Shakhnovich · Proceedings of the National Academy of Sciences · Scholar only 123 2002 Direct molecular dynamics observation of protein folding transition state ensemble Eugene I. Shakhnovich · Biophysical journal · Scholar only 167 2002 Expanding protein universe and its origin from the biological Big Bang Eugene I. Shakhnovich · Proceedings of the National Academy of Sciences · Scholar only 230 2002 Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism Eugene I. Shakhnovich · Journal of molecular biology · Scholar only 202 2002 Small molecule growth 2001 (SMoG2001): An improved knowledge-based scoring function for protein− ligand interactions Eugene I. Shakhnovich · Journal of medicinal chemistry · Scholar only 252 2002 The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation Eugene I. Shakhnovich · Proceedings of the National Academy of Sciences · Scholar only 208 2002 Topological determinants of protein folding Eugene I. Shakhnovich · Proceedings of the National Academy of Sciences · Scholar only 370 2001 Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations Eugene I. Shakhnovich · Proceedings of the National Academy of Sciences · Scholar only 130 2001 Evolutionary conservation of the folding nucleus Eugene I. Shakhnovich · Journal of molecular biology · Scholar only 172