Basin Hopping as a General and Versatile Optimization Framework for the Characterization of Biological Macromolecules

<table><tr><td><table class="algorithm" id="alg1"><tr><td colspan="2">(1) <svg height="11.4625" id="M8" style="vertical-align:-0.1638pt" version="1.1" viewbox="0 0 38.587502 11.4625" width="38.587502" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,11.2)"><path d="M244 607q0 -25 -15.5 -43t-37.5 -18q-19 0 -32 13t-13 35q0 21 15 41t39 20q20 0 32 -14t12 -34zM222 91q-29 -33 -79 -68t-75 -35q-13 0 -19 7.5t-6 31t10 65.5l62 253q5 26 -1 26q-21 0 -72 -43l-13 24q43 40 91 68t71 28q30 0 10 -78l-71 -274q-8 -30 3 -30
q16 0 76 48z" id="x1D456"></path></g><g transform="matrix(.017,-0,0,-.017,9.412,11.2)"><path d="M885 230h-727l102 -147l-22 -15q-114 125 -185 187q71 62 185 187l22 -15l-102 -147h727v-50z" id="x2190"></path></g><g transform="matrix(.017,-0,0,-.017,30.354,11.2)"><path d="M241 635q53 0 94 -28.5t63.5 -76t33.5 -102.5t11 -116q0 -58 -11 -112.5t-34 -103.5t-63.5 -78.5t-94.5 -29.5t-95 28t-64.5 75t-34.5 102.5t-11 118.5q0 58 11.5 112.5t34.5 103t64.5 78t95.5 29.5zM238 602q-32 0 -55.5 -25t-35.5 -68t-17.5 -91t-5.5 -105
q0 -76 10 -138.5t37 -107.5t69 -45q32 0 55.5 25t35.5 68.5t17.5 91.5t5.5 105t-5.5 105.5t-18 92t-36 68t-56.5 24.5z" id="x30"></path></g>
</svg></td></tr><tr><td colspan="2">(2) <svg height="15.4" id="M9" style="vertical-align:-3.3907pt" version="1.1" viewbox="0 0 17.4625 15.4" width="17.4625" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,11.112)"><path d="M775 650l-6 -28q-60 -6 -81.5 -16t-61.5 -54l-175 -191l125 -243q30 -58 48.5 -71t82.5 -19l-5 -28h-275l7 28l35 4q31 4 37 12t-6 34l-108 216q-140 -165 -177 -219q-16 -22 -10.5 -30.5t41.5 -13.5l22 -3l-7 -28h-244l8 28q52 4 75 15.5t67 52.5q48 46 206 231
l-110 215q-26 51 -44 63t-72 17l6 28h250l-6 -28l-27 -4q-30 -5 -35 -10t3 -27q17 -43 95 -190q70 78 154 185q15 21 10 29.5t-33 12.5l-30 4l5 28h236z" id="x1D44B"></path></g>
<g transform="matrix(.012,-0,0,-.012,13.525,15.187)"><path d="M244 607q0 -25 -15.5 -43t-37.5 -18q-19 0 -32 13t-13 35q0 21 15 41t39 20q20 0 32 -14t12 -34zM222 91q-29 -33 -79 -68t-75 -35q-13 0 -19 7.5t-6 31t10 65.5l62 253q5 26 -1 26q-21 0 -72 -43l-13 24q43 40 91 68t71 28q30 0 10 -78l-71 -274q-8 -30 3 -30
q16 0 76 48z" id="x1D456"></path></g>
</svg><i>←</i> random initial point in variable space</td></tr><tr><td colspan="2">(3) <svg height="15.4" id="M10" style="vertical-align:-3.3907pt" version="1.1" viewbox="0 0 15.5375 15.4" width="15.5375" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,11.112)"><path d="M667 650l-9 -28q-53 -5 -76 -17t-64 -59q-51 -61 -175 -225q-21 -29 -27 -55l-27 -136q-13 -65 -0.5 -80t83.5 -22l-7 -28h-280l8 28q64 4 81 19t30 83l25 128q6 35 -7 65l-98 231q-17 41 -32.5 52t-68.5 16l8 28h252l-6 -28l-40 -4q-27 -3 -33 -12.5t2 -31.5
q8 -26 43 -107.5t61 -134.5q114 145 174 240q14 24 8 33t-37 13l-34 4l8 28h238z" id="x1D44C"></path></g>
<g transform="matrix(.012,-0,0,-.012,11.6,15.187)"><path d="M244 607q0 -25 -15.5 -43t-37.5 -18q-19 0 -32 13t-13 35q0 21 15 41t39 20q20 0 32 -14t12 -34zM222 91q-29 -33 -79 -68t-75 -35q-13 0 -19 7.5t-6 31t10 65.5l62 253q5 26 -1 26q-21 0 -72 -43l-13 24q43 40 91 68t71 28q30 0 10 -78l-71 -274q-8 -30 3 -30
q16 0 76 48z" id="x1D456"></path></g>
</svg><i>← </i><span style="font-family:monospace">L</span><span style="font-family:monospace">OCALSEARCH</span> (<svg height="15.4" id="M11" style="vertical-align:-3.3907pt" version="1.1" viewbox="0 0 17.4625 15.4" width="17.4625" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,11.112)"><path d="M775 650l-6 -28q-60 -6 -81.5 -16t-61.5 -54l-175 -191l125 -243q30 -58 48.5 -71t82.5 -19l-5 -28h-275l7 28l35 4q31 4 37 12t-6 34l-108 216q-140 -165 -177 -219q-16 -22 -10.5 -30.5t41.5 -13.5l22 -3l-7 -28h-244l8 28q52 4 75 15.5t67 52.5q48 46 206 231
l-110 215q-26 51 -44 63t-72 17l6 28h250l-6 -28l-27 -4q-30 -5 -35 -10t3 -27q17 -43 95 -190q70 78 154 185q15 21 10 29.5t-33 12.5l-30 4l5 28h236z" id="x1D44B"></path></g>
<g transform="matrix(.012,-0,0,-.012,13.525,15.187)"><path d="M244 607q0 -25 -15.5 -43t-37.5 -18q-19 0 -32 13t-13 35q0 21 15 41t39 20q20 0 32 -14t12 -34zM222 91q-29 -33 -79 -68t-75 -35q-13 0 -19 7.5t-6 31t10 65.5l62 253q5 26 -1 26q-21 0 -72 -43l-13 24q43 40 91 68t71 28q30 0 10 -78l-71 -274q-8 -30 3 -30
q16 0 76 48z" id="x1D456"></path></g>
</svg>)</td></tr><tr><td colspan="2">(4) <b>while</b>  <span style="font-family:monospace">STOP</span> not satisfied  <b>do</b></td></tr><tr><td colspan="2">(5)   <svg height="15.4" id="M12" style="vertical-align:-3.3907pt" version="1.1" viewbox="0 0 30.15 15.4" width="30.15" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,11.112)"><path d="M775 650l-6 -28q-60 -6 -81.5 -16t-61.5 -54l-175 -191l125 -243q30 -58 48.5 -71t82.5 -19l-5 -28h-275l7 28l35 4q31 4 37 12t-6 34l-108 216q-140 -165 -177 -219q-16 -22 -10.5 -30.5t41.5 -13.5l22 -3l-7 -28h-244l8 28q52 4 75 15.5t67 52.5q48 46 206 231
l-110 215q-26 51 -44 63t-72 17l6 28h250l-6 -28l-27 -4q-30 -5 -35 -10t3 -27q17 -43 95 -190q70 78 154 185q15 21 10 29.5t-33 12.5l-30 4l5 28h236z" id="x1D44B"></path></g>
<g transform="matrix(.012,-0,0,-.012,13.525,15.187)"><path d="M244 607q0 -25 -15.5 -43t-37.5 -18q-19 0 -32 13t-13 35q0 21 15 41t39 20q20 0 32 -14t12 -34zM222 91q-29 -33 -79 -68t-75 -35q-13 0 -19 7.5t-6 31t10 65.5l62 253q5 26 -1 26q-21 0 -72 -43l-13 24q43 40 91 68t71 28q30 0 10 -78l-71 -274q-8 -30 3 -30
q16 0 76 48z" id="x1D456"></path></g><g transform="matrix(.012,-0,0,-.012,16.773,15.187)"><path d="M535 230h-212v-233h-58v233h-213v50h213v210h58v-210h212v-50z" id="x2B"></path></g><g transform="matrix(.012,-0,0,-.012,23.758,15.187)"><path d="M384 0h-275v27q67 5 81.5 18.5t14.5 68.5v385q0 38 -7.5 47.5t-40.5 10.5l-48 2v24q85 15 178 52v-521q0 -55 14.5 -68.5t82.5 -18.5v-27z" id="x31"></path></g>
</svg><i>← </i><span style="font-family:monospace">PERTURB</span> (<svg height="15.4" id="M13" style="vertical-align:-3.3907pt" version="1.1" viewbox="0 0 15.5375 15.4" width="15.5375" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,11.112)"><path d="M667 650l-9 -28q-53 -5 -76 -17t-64 -59q-51 -61 -175 -225q-21 -29 -27 -55l-27 -136q-13 -65 -0.5 -80t83.5 -22l-7 -28h-280l8 28q64 4 81 19t30 83l25 128q6 35 -7 65l-98 231q-17 41 -32.5 52t-68.5 16l8 28h252l-6 -28l-40 -4q-27 -3 -33 -12.5t2 -31.5
q8 -26 43 -107.5t61 -134.5q114 145 174 240q14 24 8 33t-37 13l-34 4l8 28h238z" id="x1D44C"></path></g>
<g transform="matrix(.012,-0,0,-.012,11.6,15.187)"><path d="M244 607q0 -25 -15.5 -43t-37.5 -18q-19 0 -32 13t-13 35q0 21 15 41t39 20q20 0 32 -14t12 -34zM222 91q-29 -33 -79 -68t-75 -35q-13 0 -19 7.5t-6 31t10 65.5l62 253q5 26 -1 26q-21 0 -72 -43l-13 24q43 40 91 68t71 28q30 0 10 -78l-71 -274q-8 -30 3 -30
q16 0 76 48z" id="x1D456"></path></g>
</svg>)</td></tr><tr><td colspan="2">(6)   <svg height="15.4" id="M14" style="vertical-align:-3.3907pt" version="1.1" viewbox="0 0 32.200001 15.4" width="32.200001" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,11.112)"><path d="M667 650l-9 -28q-53 -5 -76 -17t-64 -59q-51 -61 -175 -225q-21 -29 -27 -55l-27 -136q-13 -65 -0.5 -80t83.5 -22l-7 -28h-280l8 28q64 4 81 19t30 83l25 128q6 35 -7 65l-98 231q-17 41 -32.5 52t-68.5 16l8 28h252l-6 -28l-40 -4q-27 -3 -33 -12.5t2 -31.5
q8 -26 43 -107.5t61 -134.5q114 145 174 240q14 24 8 33t-37 13l-34 4l8 28h238z" id="x1D44C"></path></g>
<g transform="matrix(.012,-0,0,-.012,11.6,15.187)"><path d="M244 607q0 -25 -15.5 -43t-37.5 -18q-19 0 -32 13t-13 35q0 21 15 41t39 20q20 0 32 -14t12 -34zM222 91q-29 -33 -79 -68t-75 -35q-13 0 -19 7.5t-6 31t10 65.5l62 253q5 26 -1 26q-21 0 -72 -43l-13 24q43 40 91 68t71 28q30 0 10 -78l-71 -274q-8 -30 3 -30
q16 0 76 48z" id="x1D456"></path></g><g transform="matrix(.012,-0,0,-.012,14.848,15.187)"><path d="M535 230h-212v-233h-58v233h-213v50h213v210h58v-210h212v-50z" id="x2B"></path></g><g transform="matrix(.012,-0,0,-.012,21.833,15.187)"><path d="M384 0h-275v27q67 5 81.5 18.5t14.5 68.5v385q0 38 -7.5 47.5t-40.5 10.5l-48 2v24q85 15 178 52v-521q0 -55 14.5 -68.5t82.5 -18.5v-27z" id="x31"></path></g>
</svg><i>← </i><span style="font-family:monospace">LOCALSEARCH</span> (<svg height="15.4" id="M15" style="vertical-align:-3.3907pt" version="1.1" viewbox="0 0 30.15 15.4" width="30.15" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,11.112)"><path d="M775 650l-6 -28q-60 -6 -81.5 -16t-61.5 -54l-175 -191l125 -243q30 -58 48.5 -71t82.5 -19l-5 -28h-275l7 28l35 4q31 4 37 12t-6 34l-108 216q-140 -165 -177 -219q-16 -22 -10.5 -30.5t41.5 -13.5l22 -3l-7 -28h-244l8 28q52 4 75 15.5t67 52.5q48 46 206 231
l-110 215q-26 51 -44 63t-72 17l6 28h250l-6 -28l-27 -4q-30 -5 -35 -10t3 -27q17 -43 95 -190q70 78 154 185q15 21 10 29.5t-33 12.5l-30 4l5 28h236z" id="x1D44B"></path></g>
<g transform="matrix(.012,-0,0,-.012,13.525,15.187)"><path d="M244 607q0 -25 -15.5 -43t-37.5 -18q-19 0 -32 13t-13 35q0 21 15 41t39 20q20 0 32 -14t12 -34zM222 91q-29 -33 -79 -68t-75 -35q-13 0 -19 7.5t-6 31t10 65.5l62 253q5 26 -1 26q-21 0 -72 -43l-13 24q43 40 91 68t71 28q30 0 10 -78l-71 -274q-8 -30 3 -30
q16 0 76 48z" id="x1D456"></path></g><g transform="matrix(.012,-0,0,-.012,16.773,15.187)"><path d="M535 230h-212v-233h-58v233h-213v50h213v210h58v-210h212v-50z" id="x2B"></path></g><g transform="matrix(.012,-0,0,-.012,23.758,15.187)"><path d="M384 0h-275v27q67 5 81.5 18.5t14.5 68.5v385q0 38 -7.5 47.5t-40.5 10.5l-48 2v24q85 15 178 52v-521q0 -55 14.5 -68.5t82.5 -18.5v-27z" id="x31"></path></g>
</svg>)</td></tr><tr><td colspan="2">(7)   <b>if</b>  <svg height="16.6625" id="M16" style="vertical-align:-3.56265pt" version="1.1" viewbox="0 0 108.425 16.6625" width="108.425" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,12.162)"><path d="M619 670q0 -13 -9 -26t-18 -19q-13 -10 -25 2q-36 38 -66 38q-31 0 -54.5 -50t-45.5 -185h120l-20 -31l-107 -12q-23 -138 -57 -293q-27 -122 -55 -184.5t-75 -109.5q-60 -61 -114 -61q-25 0 -47.5 15t-22.5 31q0 17 31 44q11 8 20 -1q10 -11 31 -19t35 -8q26 0 47 19
q34 34 71 253l54 315h-90l-3 12l31 30h70q28 138 90 204q35 37 75 57.5t70 20.5q26 0 45 -14t19 -28z" id="x1D453"></path></g><g transform="matrix(.017,-0,0,-.017,10.976,12.162)"><path d="M300 -147l-18 -23q-106 71 -159 185.5t-53 254.5v1q0 139 53 252.5t159 186.5l18 -24q-74 -62 -115.5 -173.5t-41.5 -242.5q0 -130 41.5 -242.5t115.5 -174.5z" id="x28"></path></g><g transform="matrix(.017,-0,0,-.017,16.857,12.162)"><path d="M667 650l-9 -28q-53 -5 -76 -17t-64 -59q-51 -61 -175 -225q-21 -29 -27 -55l-27 -136q-13 -65 -0.5 -80t83.5 -22l-7 -28h-280l8 28q64 4 81 19t30 83l25 128q6 35 -7 65l-98 231q-17 41 -32.5 52t-68.5 16l8 28h252l-6 -28l-40 -4q-27 -3 -33 -12.5t2 -31.5
q8 -26 43 -107.5t61 -134.5q114 145 174 240q14 24 8 33t-37 13l-34 4l8 28h238z" id="x1D44C"></path></g>
<g transform="matrix(.012,-0,0,-.012,28.4,16.25)"><path d="M244 607q0 -25 -15.5 -43t-37.5 -18q-19 0 -32 13t-13 35q0 21 15 41t39 20q20 0 32 -14t12 -34zM222 91q-29 -33 -79 -68t-75 -35q-13 0 -19 7.5t-6 31t10 65.5l62 253q5 26 -1 26q-21 0 -72 -43l-13 24q43 40 91 68t71 28q30 0 10 -78l-71 -274q-8 -30 3 -30
q16 0 76 48z" id="x1D456"></path></g><g transform="matrix(.012,-0,0,-.012,31.648,16.25)"><path d="M535 230h-212v-233h-58v233h-213v50h213v210h58v-210h212v-50z" id="x2B"></path></g><g transform="matrix(.012,-0,0,-.012,38.633,16.25)"><path d="M384 0h-275v27q67 5 81.5 18.5t14.5 68.5v385q0 38 -7.5 47.5t-40.5 10.5l-48 2v24q85 15 178 52v-521q0 -55 14.5 -68.5t82.5 -18.5v-27z" id="x31"></path></g>
<g transform="matrix(.017,-0,0,-.017,44.962,12.162)"><path d="M275 270q0 -296 -211 -440l-19 23q75 62 116.5 174t41.5 243t-42 243t-116 173l19 24q211 -144 211 -440z" id="x29"></path></g><g transform="matrix(.017,-0,0,-.017,55.57,12.162)"><path d="M512 -3l-437 233v51l437 233v-58l-378 -200v-2l378 -199v-58z" id="x3C"></path></g><g transform="matrix(.017,-0,0,-.017,70.257,12.162)"><path d="M619 670q0 -13 -9 -26t-18 -19q-13 -10 -25 2q-36 38 -66 38q-31 0 -54.5 -50t-45.5 -185h120l-20 -31l-107 -12q-23 -138 -57 -293q-27 -122 -55 -184.5t-75 -109.5q-60 -61 -114 -61q-25 0 -47.5 15t-22.5 31q0 17 31 44q11 8 20 -1q10 -11 31 -19t35 -8q26 0 47 19
q34 34 71 253l54 315h-90l-3 12l31 30h70q28 138 90 204q35 37 75 57.5t70 20.5q26 0 45 -14t19 -28z" id="x1D453"></path></g><g transform="matrix(.017,-0,0,-.017,81.17,12.162)"><path d="M300 -147l-18 -23q-106 71 -159 185.5t-53 254.5v1q0 139 53 252.5t159 186.5l18 -24q-74 -62 -115.5 -173.5t-41.5 -242.5q0 -130 41.5 -242.5t115.5 -174.5z" id="x28"></path></g><g transform="matrix(.017,-0,0,-.017,87.051,12.162)"><path d="M667 650l-9 -28q-53 -5 -76 -17t-64 -59q-51 -61 -175 -225q-21 -29 -27 -55l-27 -136q-13 -65 -0.5 -80t83.5 -22l-7 -28h-280l8 28q64 4 81 19t30 83l25 128q6 35 -7 65l-98 231q-17 41 -32.5 52t-68.5 16l8 28h252l-6 -28l-40 -4q-27 -3 -33 -12.5t2 -31.5
q8 -26 43 -107.5t61 -134.5q114 145 174 240q14 24 8 33t-37 13l-34 4l8 28h238z" id="x1D44C"></path></g>
<g transform="matrix(.012,-0,0,-.012,98.612,16.25)"><path d="M244 607q0 -25 -15.5 -43t-37.5 -18q-19 0 -32 13t-13 35q0 21 15 41t39 20q20 0 32 -14t12 -34zM222 91q-29 -33 -79 -68t-75 -35q-13 0 -19 7.5t-6 31t10 65.5l62 253q5 26 -1 26q-21 0 -72 -43l-13 24q43 40 91 68t71 28q30 0 10 -78l-71 -274q-8 -30 3 -30
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<g transform="matrix(.017,-0,0,-.017,102.475,12.162)"><path d="M275 270q0 -296 -211 -440l-19 23q75 62 116.5 174t41.5 243t-42 243t-116 173l19 24q211 -144 211 -440z" id="x29"></path></g>
</svg>  <b>then</b></td></tr><tr><td colspan="2">(8)    <svg height="11.4625" id="M17" style="vertical-align:-0.1638pt" version="1.1" viewbox="0 0 60.762501 11.4625" width="60.762501" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,11.2)"><path d="M244 607q0 -25 -15.5 -43t-37.5 -18q-19 0 -32 13t-13 35q0 21 15 41t39 20q20 0 32 -14t12 -34zM222 91q-29 -33 -79 -68t-75 -35q-13 0 -19 7.5t-6 31t10 65.5l62 253q5 26 -1 26q-21 0 -72 -43l-13 24q43 40 91 68t71 28q30 0 10 -78l-71 -274q-8 -30 3 -30
q16 0 76 48z" id="x1D456"></path></g><g transform="matrix(.017,-0,0,-.017,9.412,11.2)"><path d="M885 230h-727l102 -147l-22 -15q-114 125 -185 187q71 62 185 187l22 -15l-102 -147h727v-50z" id="x2190"></path></g><g transform="matrix(.017,-0,0,-.017,30.354,11.2)"><path d="M244 607q0 -25 -15.5 -43t-37.5 -18q-19 0 -32 13t-13 35q0 21 15 41t39 20q20 0 32 -14t12 -34zM222 91q-29 -33 -79 -68t-75 -35q-13 0 -19 7.5t-6 31t10 65.5l62 253q5 26 -1 26q-21 0 -72 -43l-13 24q43 40 91 68t71 28q30 0 10 -78l-71 -274q-8 -30 3 -30
q16 0 76 48z" id="x1D456"></path></g><g transform="matrix(.017,-0,0,-.017,38.769,11.2)"><path d="M535 230h-212v-233h-58v233h-213v50h213v210h58v-210h212v-50z" id="x2B"></path></g><g transform="matrix(.017,-0,0,-.017,52.521,11.2)"><path d="M384 0h-275v27q67 5 81.5 18.5t14.5 68.5v385q0 38 -7.5 47.5t-40.5 10.5l-48 2v24q85 15 178 52v-521q0 -55 14.5 -68.5t82.5 -18.5v-27z" id="x31"></path></g>
</svg></td></tr></table></td></tr></table>

Advances in Artificial Intelligence

alg1

Algorithm 1

Algorithm 1: Basin Hopping as a General and Versatile Optimization Framework for the Characterization of Biological Macromolecules 